rs4922505

Variant names:

• chr10-47317214-G-A
• rs4922505

Your query was ambiguous. Multiple possible variants found:

• chr10-47317214-G-A
• chr10-47317214-G-C
• chr10-47317214-G-T

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 0.967 in 152,370 control chromosomes in the GnomAD database, including 71,310 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 0.97 (71310 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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: 0.967 AC: 147268 AN: 152252 Hom.: 71261 Cov.: 35

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.967 AC: 147376 AN: 152370 Hom.: 71310 Cov.: 35 AF XY: 0.966 AC XY: 71966 AN XY: 74508

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.976

Alfa AF: 0.968 Hom.: 10942

Bravo AF: 0.964

Asia WGS AF: 0.922 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4922505; hg19: chr10-48422148;