rs263906

Variant names:

• chr1-101512778-T-C
• rs263906

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.697 AC: 28899 AN: 41446

American (AMR) AF: 0.594 AC: 9055 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2658 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3051 AN: 5160

South Asian (SAS) AF: 0.620 AC: 2978 AN: 4806

European-Finnish (FIN) AF: 0.766 AC: 8079 AN: 10546

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50949 AN: 67960

Other (OTH) AF: 0.734 AC: 1544 AN: 2104

Alfa AF: 0.718 Hom.: 23166

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs263906; hg19: chr1-101978334;