rs275646

chr3-148745735-T-C

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 0.948 in 150,984 control chromosomes in the GnomAD database, including 67,932 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 0.95 (67932 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.948 AC: 142991 AN: 150868 Hom.: 67899 Cov.: 28

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.917

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.948 AC: 143083 AN: 150984 Hom.: 67932 Cov.: 28 AF XY: 0.945 AC XY: 69697 AN XY: 73788

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.943

Alfa AF: 0.953 Hom.: 12125

Bravo AF: 0.953

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275646; hg19: chr3-148463522;