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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.281 AC: 11639 AN: 41408

American (AMR) AF: 0.415 AC: 6325 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3466

East Asian (EAS) AF: 0.260 AC: 1335 AN: 5136

South Asian (SAS) AF: 0.464 AC: 2233 AN: 4812

European-Finnish (FIN) AF: 0.530 AC: 5561 AN: 10500

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.502 AC: 34042 AN: 67766

Other (OTH) AF: 0.464 AC: 977 AN: 2104

Alfa AF: 0.479 Hom.: 22190

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
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs534371; hg19: chr10-29441360;