3-152770251-T-C

Variant names:

• chr3-152770251-T-C
• rs9875837

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 0.581 in 151,852 control chromosomes in the GnomAD database, including 26,976 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 0.58 (26976 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

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 (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.582 AC: 88244 AN: 151734 Hom.: 26962 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.581 AC: 88287 AN: 151852 Hom.: 26976 Cov.: 31 AF XY: 0.584 AC XY: 43327 AN XY: 74242

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.593

Alfa AF: 0.642 Hom.: 14572

Bravo AF: 0.573

Asia WGS AF: 0.717 AC: 2490 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9875837; hg19: chr3-152488040;