chr3-154998568-T-C

Variant names:

• chr3-154998568-T-C
• rs2314612

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 0.449 in 152,060 control chromosomes in the GnomAD database, including 18,449 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 0.45 (18449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68306 AN: 151942 Hom.: 18450 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.449 AC: 68310 AN: 152060 Hom.: 18449 Cov.: 32 AF XY: 0.449 AC XY: 33386 AN XY: 74334

African (AFR) AF: 0.131 AC: 5449 AN: 41496

American (AMR) AF: 0.516 AC: 7876 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2681 AN: 5158

South Asian (SAS) AF: 0.391 AC: 1886 AN: 4818

European-Finnish (FIN) AF: 0.576 AC: 6074 AN: 10554

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40178 AN: 67986

Other (OTH) AF: 0.505 AC: 1067 AN: 2112

Alfa AF: 0.541 Hom.: 30415

Bravo AF: 0.433

Asia WGS AF: 0.425 AC: 1478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs2314612; hg19: chr3-154716357;