3-24072206-T-C

Position:

• chr3-24072206-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 0.736 in 152,006 control chromosomes in the GnomAD database, including 41,291 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 0.74 (41291 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111768 AN: 151888 Hom.: 41265 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.736 AC: 111847 AN: 152006 Hom.: 41291 Cov.: 30 AF XY: 0.733 AC XY: 54474 AN XY: 74284

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.729

Alfa AF: 0.744 Hom.: 55910

Bravo AF: 0.727

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6801153; hg19: chr3-24113697;