rs275646

Variant names:

• chr3-148745735-T-C
• rs275646

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 0.948 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.942 AC: 38830 AN: 41226

American (AMR) AF: 0.966 AC: 14677 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3352 AN: 3462

East Asian (EAS) AF: 0.846 AC: 4362 AN: 5156

South Asian (SAS) AF: 0.768 AC: 3674 AN: 4786

European-Finnish (FIN) AF: 0.965 AC: 9703 AN: 10052

Middle Eastern (MID) AF: 0.914 AC: 267 AN: 292

European-Non Finnish (NFE) AF: 0.964 AC: 65350 AN: 67814

Other (OTH) AF: 0.943 AC: 1979 AN: 2098

Alfa AF: 0.956 Hom.: 93056

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs275646; hg19: chr3-148463522;