chr3-148601446-A-T

Variant names:

• chr3-148601446-A-T
• rs2687661

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 0.407 in 151,960 control chromosomes in the GnomAD database, including 13,104 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 0.41 (13104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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: 0.407 AC: 61728 AN: 151842 Hom.: 13079 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.407 AC: 61793 AN: 151960 Hom.: 13104 Cov.: 32 AF XY: 0.407 AC XY: 30212 AN XY: 74262

African (AFR) AF: 0.538 AC: 22274 AN: 41432

American (AMR) AF: 0.320 AC: 4885 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2388 AN: 5146

South Asian (SAS) AF: 0.425 AC: 2043 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4357 AN: 10584

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23296 AN: 67944

Other (OTH) AF: 0.384 AC: 811 AN: 2114

Alfa AF: 0.378 Hom.: 1446

Bravo AF: 0.408

Asia WGS AF: 0.459 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.35
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2687661; hg19: chr3-148319233;