rs365238

Variant names:

• chr3-172524076-C-T
• rs365238

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 0.884 in 152,238 control chromosomes in the GnomAD database, including 59,672 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 0.88 (59672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.884 AC: 134548 AN: 152120 Hom.: 59624 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.884 AC: 134654 AN: 152238 Hom.: 59672 Cov.: 32 AF XY: 0.886 AC XY: 65982 AN XY: 74436

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.886

Alfa AF: 0.869 Hom.: 76584

Bravo AF: 0.887

Asia WGS AF: 0.929 AC: 3228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs365238; hg19: chr3-172241866;