chr1-94131311-A-G

Variant names:

• chr1-94131311-A-G
• rs1931565

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 0.68 in 152,132 control chromosomes in the GnomAD database, including 35,567 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 0.68 (35567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 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: 0.680 AC: 103407 AN: 152010 Hom.: 35540 Cov.: 33

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.680 AC: 103495 AN: 152132 Hom.: 35567 Cov.: 33 AF XY: 0.678 AC XY: 50449 AN XY: 74380

African (AFR) AF: 0.760 AC: 31549 AN: 41498

American (AMR) AF: 0.680 AC: 10389 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2091 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3814 AN: 5178

South Asian (SAS) AF: 0.584 AC: 2819 AN: 4828

European-Finnish (FIN) AF: 0.633 AC: 6703 AN: 10582

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44094 AN: 67986

Other (OTH) AF: 0.655 AC: 1383 AN: 2110

Alfa AF: 0.654 Hom.: 139584

Bravo AF: 0.685

Asia WGS AF: 0.696 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1931565; hg19: chr1-94596867;