chr3-5270778-C-T

Variant names:

• chr3-5270778-C-T
• rs2173488

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 0.454 in 152,078 control chromosomes in the GnomAD database, including 18,492 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 (18492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 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: 0.455 AC: 69096 AN: 151960 Hom.: 18493 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.454 AC: 69090 AN: 152078 Hom.: 18492 Cov.: 32 AF XY: 0.452 AC XY: 33610 AN XY: 74332

African (AFR) AF: 0.188 AC: 7824 AN: 41510

American (AMR) AF: 0.424 AC: 6482 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1708 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1313 AN: 5174

South Asian (SAS) AF: 0.370 AC: 1786 AN: 4822

European-Finnish (FIN) AF: 0.622 AC: 6558 AN: 10548

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41866 AN: 67958

Other (OTH) AF: 0.471 AC: 996 AN: 2114

Alfa AF: 0.577 Hom.: 11444

Bravo AF: 0.424

Asia WGS AF: 0.286 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.82
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2173488; hg19: chr3-5312463; COSMIC: COSV69676566;