chr1-94131311-A-G

Variant names:

• chr1-94131311-A-G
• rs1931565

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 0.68 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.655

Alfa AF: 0.646 Hom.: 64738

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931565; hg19: chr1-94596867;