3-149460874-G-T

Variant names:

• chr3-149460874-G-T
• rs4405858

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 0.935 in 152,226 control chromosomes in the GnomAD database, including 66,751 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 0.94 (66751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 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: 0.935 AC: 142289 AN: 152108 Hom.: 66696 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.935 AC: 142403 AN: 152226 Hom.: 66751 Cov.: 32 AF XY: 0.933 AC XY: 69458 AN XY: 74414

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.935

Alfa AF: 0.929 Hom.: 135285

Bravo AF: 0.941

Asia WGS AF: 0.870 AC: 3023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.37
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: rs4405858; hg19: chr3-149178661;