10-100881934-G-A

Variant names:

• chr10-100881934-G-A
• rs1467616

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 0.597 in 152,148 control chromosomes in the GnomAD database, including 27,643 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 0.60 (27643 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90750 AN: 152030 Hom.: 27631 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.597 AC: 90800 AN: 152148 Hom.: 27643 Cov.: 33 AF XY: 0.594 AC XY: 44204 AN XY: 74368

African (AFR) AF: 0.498 AC: 20692 AN: 41512

American (AMR) AF: 0.634 AC: 9685 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1773 AN: 5170

South Asian (SAS) AF: 0.580 AC: 2793 AN: 4818

European-Finnish (FIN) AF: 0.641 AC: 6783 AN: 10588

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.657 AC: 44643 AN: 67982

Other (OTH) AF: 0.614 AC: 1299 AN: 2116

Alfa AF: 0.633 Hom.: 57435

Bravo AF: 0.589

Asia WGS AF: 0.474 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.16
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs1467616; hg19: chr10-102641691;