chr6-87472721-T-C

Position:

• chr6-87472721-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XR_007059668.1(LOC124901357):​n.173+52A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,124 control chromosomes in the GnomAD database, including 28,139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.60 (28139 hom., cov: 33)
• Consequence: LOC124901357 XR_007059668.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.01

Genes affected

LOC124901357 (HGNC:):

SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 6-87472721-T-C is Benign according to our data. Variant chr6-87472721-T-C is described in ClinVar as [Benign]. Clinvar id is 1259892.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901357	XR_007059668.1	n.173+52A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000464978.5	n.91+2008T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91100 AN: 152006 Hom.: 28090 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.600 AC: 91210 AN: 152124 Hom.: 28139 Cov.: 33 AF XY: 0.597 AC XY: 44366 AN XY: 74372

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.588

Alfa AF: 0.547 Hom.: 21958

Bravo AF: 0.622

Asia WGS AF: 0.612 AC: 2126 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs2273129; hg19: chr6-88182439;