10-92722160-G-A

Variant names:

• chr10-92722160-G-A
• rs7923837

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 0.327 in 147,190 control chromosomes in the GnomAD database, including 9,841 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 0.33 (9841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 168 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.327 AC: 48094 AN: 147068 Hom.: 9842 Cov.: 31

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.327 AC: 48106 AN: 147190 Hom.: 9841 Cov.: 31 AF XY: 0.335 AC XY: 23948 AN XY: 71522

African (AFR) AF: 0.0846 AC: 3404 AN: 40238

American (AMR) AF: 0.397 AC: 5698 AN: 14340

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1253 AN: 3430

East Asian (EAS) AF: 0.807 AC: 4170 AN: 5168

South Asian (SAS) AF: 0.566 AC: 2632 AN: 4654

European-Finnish (FIN) AF: 0.426 AC: 4109 AN: 9648

Middle Eastern (MID) AF: 0.282 AC: 80 AN: 284

European-Non Finnish (NFE) AF: 0.385 AC: 25619 AN: 66536

Other (OTH) AF: 0.350 AC: 700 AN: 1998

Alfa AF: 0.364 Hom.: 45376

Bravo AF: 0.309

Asia WGS AF: 0.583 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7923837; hg19: chr10-94481917;