Variant 8-120157961-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_021110.4(COL14A1):c.89-169G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,002 control chromosomes in the GnomAD database, including 15,126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 15126 hom., cov: 32)

Consequence

COL14A1
NM_021110.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.191

Variant links:

Genes affected

COL14A1 (HGNC:2191): (collagen type XIV alpha 1 chain) This gene encodes the alpha chain of type XIV collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XIV collagen interacts with the fibril surface and is involved in the regulation of fibrillogenesis. [provided by RefSeq, Jan 2013]

COL14A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 8-120157961-G-T is Benign according to our data. Variant chr8-120157961-G-T is described in ClinVar as [Benign]. Clinvar id is 1222432.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL14A1	NM_021110.4 link	c.89-169G>T		intron_variant		ENST00000297848.8	NP_066933.1	Q05707-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL14A1	ENST00000297848.8 link	c.89-169G>T		intron_variant		5	NM_021110.4	ENSP00000297848.3		Q05707-1

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

63034

AN:

151884

Hom.:

15112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.344

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.415

AC:

63101

AN:

152002

Hom.:

15126

Cov.:

AF XY:

0.417

AC XY:

30985

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.664

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.368

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.486

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.366

Hom.:

1407

Bravo

AF:

0.415

Asia WGS

AF:

0.374

AC:

1301

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.63

DANN

Benign

0.55

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