3-141940399-C-T

Position:

• chr3-141940399-C-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 0.723 in 152,174 control chromosomes in the GnomAD database, including 39,903 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 0.72 (39903 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.141940399C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109978 AN: 152056 Hom.: 39888 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.723 AC: 110040 AN: 152174 Hom.: 39903 Cov.: 33 AF XY: 0.727 AC XY: 54071 AN XY: 74404

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.732

Alfa AF: 0.732 Hom.: 84713

Bravo AF: 0.720

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6440052; hg19: chr3-141659241;