rs10485131

Variant names:

• chr6-78597647-G-A
• rs10485131
• ENST00000715178.1:n.331+6876C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000715178.1(ENSG00000230309):​n.331+6876C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,228 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.022 (62 hom., cov: 33)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 2 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0224 (3411/152228) while in subpopulation SAS AF = 0.0413 (199/4818). AF 95% confidence interval is 0.0366. There are 62 homozygotes in GnomAd4. There are 1669 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 62 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1	n.331+6876C>T		intron_variant	Intron 2 of 14
ENSG00000230309	ENST00000830453.1	n.119+6876C>T		intron_variant	Intron 2 of 2
ENSG00000230309	ENST00000830454.1	n.160+6876C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3412 AN: 152110 Hom.: 62 Cov.: 33

Gnomad AFR AF: 0.00577

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0224 AC: 3411 AN: 152228 Hom.: 62 Cov.: 33 AF XY: 0.0224 AC XY: 1669 AN XY: 74428

African (AFR) AF: 0.00575 AC: 239 AN: 41558

American (AMR) AF: 0.0199 AC: 304 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4818

European-Finnish (FIN) AF: 0.0190 AC: 202 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0347 AC: 2362 AN: 67994

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0327 Hom.: 60

Bravo AF: 0.0217

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.68
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs10485131; hg19: chr6-79307364;