3-149460874-G-T

Variant names:

• chr3-149460874-G-T
• rs4405858

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 0.935 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.972 AC: 40348 AN: 41518

American (AMR) AF: 0.954 AC: 14587 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3004 AN: 3470

East Asian (EAS) AF: 0.772 AC: 3992 AN: 5174

South Asian (SAS) AF: 0.884 AC: 4266 AN: 4826

European-Finnish (FIN) AF: 0.927 AC: 9833 AN: 10606

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63295 AN: 68014

Other (OTH) AF: 0.935 AC: 1979 AN: 2116

Alfa AF: 0.930 Hom.: 289592

Bravo AF: 0.941

Asia WGS AF: 0.870 AC: 3023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.37
DANN	Benign	0.52
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4405858; hg19: chr3-149178661;