rs263906

Variant names:

• chr1-101512778-T-C
• rs263906

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.712 in 151,930 control chromosomes in the GnomAD database, including 38,932 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 0.71 (38932 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

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

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108106 AN: 151812 Hom.: 38908 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.712 AC: 108180 AN: 151930 Hom.: 38932 Cov.: 31 AF XY: 0.710 AC XY: 52726 AN XY: 74230

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.734

Alfa AF: 0.713 Hom.: 15129

Bravo AF: 0.696

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs263906; hg19: chr1-101978334;