rs12638075

chr3-140703546-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 0.0249 in 152,290 control chromosomes in the GnomAD database, including 79 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 0.025 (79 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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: 0.0247 AC: 3765 AN: 152172 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0224

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

GnomAD4 genome AF: 0.0249 AC: 3796 AN: 152290 Hom.: 79 Cov.: 32 AF XY: 0.0252 AC XY: 1876 AN XY: 74468

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0232

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.0188

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0196 Hom.: 49

Bravo AF: 0.0271

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	7.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12638075; hg19: chr3-140422388;