3-152770251-T-C

Position:

• chr3-152770251-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.152770251T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;