rs10777629

Variant names:

• chr12-94820273-G-A
• rs10777629
• ENST00000798087.1:n.83-26761C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-94820273-G-A
• chr12-94820273-G-C
• chr12-94820273-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000798087.1(ENSG00000303924):​n.83-26761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,126 control chromosomes in the GnomAD database, including 51,341 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 0.82 (51341 hom., cov: 31)
• Consequence: ENSG00000303924 ENST00000798087.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 5 publications found

Genes affected

ENSG00000303924 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798087.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303924	ENST00000798087.1		n.83-26761C>T		intron	N/A
	ENSG00000303924	ENST00000798088.1		n.26-21683C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124795 AN: 152008 Hom.: 51282 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.821 AC: 124915 AN: 152126 Hom.: 51341 Cov.: 31 AF XY: 0.826 AC XY: 61390 AN XY: 74348

African (AFR) AF: 0.831 AC: 34489 AN: 41502

American (AMR) AF: 0.884 AC: 13502 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2714 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4616 AN: 5178

South Asian (SAS) AF: 0.801 AC: 3858 AN: 4816

European-Finnish (FIN) AF: 0.850 AC: 8993 AN: 10580

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54077 AN: 67998

Other (OTH) AF: 0.829 AC: 1748 AN: 2108

Alfa AF: 0.804 Hom.: 209110

Bravo AF: 0.825

Asia WGS AF: 0.854 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.67
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10777629; hg19: chr12-95214049;