rs4922536

Variant names:

• chr10-47190985-A-C
• rs4922536

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 0.486 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.486 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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.491

Alfa AF: 0.511 Hom.: 35500

Bravo AF: 0.479

Asia WGS AF: 0.580 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.0020
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4922536; hg19: chr10-48548377;