chr3-24071761-T-C

Position:

• chr3-24071761-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 0.394 in 152,096 control chromosomes in the GnomAD database, including 13,092 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 0.39 (13092 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24071761T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59920 AN: 151978 Hom.: 13071 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.394 AC: 59984 AN: 152096 Hom.: 13092 Cov.: 32 AF XY: 0.396 AC XY: 29434 AN XY: 74336

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.361

Alfa AF: 0.356 Hom.: 1273

Bravo AF: 0.403

Asia WGS AF: 0.457 AC: 1587 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	3.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6800768; hg19: chr3-24113252;