3-5270778-C-T

Variant names:

• chr3-5270778-C-T
• rs2173488

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 0.454 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.455 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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.471

Alfa AF: 0.566 Hom.: 5974

Bravo AF: 0.424

Asia WGS AF: 0.286 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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