dbSNP rs582736: CHST14:c.*6G>A (chr15-40472350-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_130468.4(CHST14):c.*6G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 1,589,784 control chromosomes in the GnomAD database, including 7,958 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1927 hom., cov: 32)

Exomes 𝑓: 0.083 ( 6031 hom. )

Consequence

CHST14
NM_130468.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.31

Variant links:

Genes affected

CHST14 (HGNC:24464): (carbohydrate sulfotransferase 14) This gene encodes a member of the HNK-1 family of sulfotransferases. The encoded protein transfers sulfate to the C-4 hydroxyl of N-acetylgalactosamine residues in dermatan sulfate. Mutations in this gene have been associated with adducted thumb-clubfoot syndrome.[provided by RefSeq, Mar 2010]

CHST14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 15-40472350-G-A is Benign according to our data. Variant chr15-40472350-G-A is described in ClinVar as [Benign]. Clinvar id is 128769.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST14	NM_130468.4 link	c.*6G>A		3_prime_UTR_variant	Exon 1 of 1	ENST00000306243.7	NP_569735.1	Q8NCH0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST14	ENST00000306243.7 link	c.*6G>A		3_prime_UTR_variant	Exon 1 of 1	6	NM_130468.4	ENSP00000307297.6		Q8NCH0
CHST14	ENST00000559991.1 link	c.*6G>A		3_prime_UTR_variant	Exon 2 of 2	5		ENSP00000453882.1		H0YN65

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20531

AN:

152142

Hom.:

1916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0795

Gnomad ASJ

AF:

0.0403

Gnomad EAS

AF:

0.0961

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.0831

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0821

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0980

AC:

22732

AN:

231868

Hom.:

1491

AF XY:

0.0969

AC XY:

12096

AN XY:

124806

show subpopulations

Gnomad AFR exome

AF:

0.278

Gnomad AMR exome

AF:

0.0790

Gnomad ASJ exome

AF:

0.0386

Gnomad EAS exome

AF:

0.0953

Gnomad SAS exome

AF:

0.131

Gnomad FIN exome

AF:

0.0807

Gnomad NFE exome

AF:

0.0778

Gnomad OTH exome

AF:

0.0798

GnomAD4 exome

AF:

0.0834

AC:

119885

AN:

1437524

Hom.:

6031

Cov.:

AF XY:

0.0848

AC XY:

60366

AN XY:

712278

show subpopulations

Gnomad4 AFR exome

AF:

0.276

Gnomad4 AMR exome

AF:

0.0791

Gnomad4 ASJ exome

AF:

0.0404

Gnomad4 EAS exome

AF:

0.0789

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.0801

Gnomad4 NFE exome

AF:

0.0750

Gnomad4 OTH exome

AF:

0.0914

GnomAD4 genome

AF:

0.135

AC:

20578

AN:

152260

Hom.:

1927

Cov.:

AF XY:

0.133

AC XY:

9900

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.272

Gnomad4 AMR

AF:

0.0796

Gnomad4 ASJ

AF:

0.0403

Gnomad4 EAS

AF:

0.0957

Gnomad4 SAS

AF:

0.129

Gnomad4 FIN

AF:

0.0831

Gnomad4 NFE

AF:

0.0821

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.0932

Hom.:

1038

Bravo

AF:

0.141

Asia WGS

AF:

0.111

AC:

384

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Oct 06, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Aug 15, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.9

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over