rs4922536

Variant names:

• chr10-47190985-A-C
• rs4922536

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 0.486 in 151,864 control chromosomes in the GnomAD database, including 18,522 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 0.49 (18522 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 1 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 = 0.746 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73727 AN: 151746 Hom.: 18517 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.486 AC: 73759 AN: 151864 Hom.: 18522 Cov.: 31 AF XY: 0.488 AC XY: 36224 AN XY: 74222

African (AFR) AF: 0.391 AC: 16172 AN: 41362

American (AMR) AF: 0.470 AC: 7163 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3949 AN: 5158

South Asian (SAS) AF: 0.532 AC: 2566 AN: 4822

European-Finnish (FIN) AF: 0.524 AC: 5525 AN: 10544

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35064 AN: 67938

Other (OTH) AF: 0.491 AC: 1036 AN: 2112

Alfa AF: 0.503 Hom.: 55790

Bravo AF: 0.479

Asia WGS AF: 0.580 AC: 2015 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	0.0020
DANN	Benign	0.44
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4922536; hg19: chr10-48548377;