chr3-158907015-C-T

Variant names:

• chr3-158907015-C-T
• rs414357

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 0.489 in 151,994 control chromosomes in the GnomAD database, including 19,164 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 0.49 (19164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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: 0.489 AC: 74231 AN: 151876 Hom.: 19148 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.489 AC: 74271 AN: 151994 Hom.: 19164 Cov.: 32 AF XY: 0.491 AC XY: 36473 AN XY: 74296

African (AFR) AF: 0.327 AC: 13555 AN: 41458

American (AMR) AF: 0.554 AC: 8462 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1775 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3530 AN: 5144

South Asian (SAS) AF: 0.501 AC: 2414 AN: 4822

European-Finnish (FIN) AF: 0.595 AC: 6295 AN: 10588

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36593 AN: 67934

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.508 Hom.: 24452

Bravo AF: 0.483

Asia WGS AF: 0.584 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.52
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs414357; hg19: chr3-158624804;