3-148601039-C-T

Variant names:

• chr3-148601039-C-T
• rs1357424

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 0.325 in 151,950 control chromosomes in the GnomAD database, including 9,087 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 0.32 (9087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49320 AN: 151836 Hom.: 9087 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.325 AC: 49325 AN: 151950 Hom.: 9087 Cov.: 32 AF XY: 0.321 AC XY: 23865 AN XY: 74246

African (AFR) AF: 0.140 AC: 5793 AN: 41484

American (AMR) AF: 0.354 AC: 5396 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1346 AN: 5148

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4810

European-Finnish (FIN) AF: 0.368 AC: 3885 AN: 10560

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28926 AN: 67918

Other (OTH) AF: 0.337 AC: 711 AN: 2112

Alfa AF: 0.367 Hom.: 1671

Bravo AF: 0.314

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs1357424; hg19: chr3-148318826;