3-148601446-A-T

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 0.407 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.384

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2687661; hg19: chr3-148319233;