rs10863681

Variant names:

• chr1-222071916-A-G
• rs10863681

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 0.478 in 152,090 control chromosomes in the GnomAD database, including 17,629 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 0.48 (17629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 7 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.478 AC: 72645 AN: 151972 Hom.: 17618 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.478 AC: 72681 AN: 152090 Hom.: 17629 Cov.: 32 AF XY: 0.474 AC XY: 35224 AN XY: 74328

African (AFR) AF: 0.557 AC: 23084 AN: 41478

American (AMR) AF: 0.445 AC: 6800 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3472

East Asian (EAS) AF: 0.446 AC: 2306 AN: 5166

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4820

European-Finnish (FIN) AF: 0.401 AC: 4242 AN: 10576

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31546 AN: 67978

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.472 Hom.: 18193

Bravo AF: 0.485

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.58
DANN	Benign	0.75
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10863681; hg19: chr1-222245258;