rs534371

Variant names:

• chr10-29152431-A-G
• rs534371

Your query was ambiguous. Multiple possible variants found:

• chr10-29152431-A-G
• chr10-29152431-A-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 0.425 in 151,624 control chromosomes in the GnomAD database, including 14,479 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 0.42 (14479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 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: 0.425 AC: 64406 AN: 151506 Hom.: 14484 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.425 AC: 64410 AN: 151624 Hom.: 14479 Cov.: 32 AF XY: 0.426 AC XY: 31522 AN XY: 74064

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.464

Alfa AF: 0.489 Hom.: 17430

Bravo AF: 0.408

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs534371; hg19: chr10-29441360;