rs4301693

Variant names:

• chr10-32149271-G-A
• rs4301693

Your query was ambiguous. Multiple possible variants found:

• chr10-32149271-G-A
• chr10-32149271-G-C
• chr10-32149271-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 0.179 in 152,128 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.179 AC: 27232 AN: 152010 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27270 AN: 152128 Hom.: 2640 Cov.: 32 AF XY: 0.181 AC XY: 13493 AN XY: 74368

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.194

Alfa AF: 0.147 Hom.: 1129

Bravo AF: 0.184

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4301693; hg19: chr10-32438199;