3-24071761-T-C

Variant names:

• chr3-24071761-T-C
• rs6800768

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 0.394 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.580 AC: 24055 AN: 41480

American (AMR) AF: 0.333 AC: 5089 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3045 AN: 5174

South Asian (SAS) AF: 0.285 AC: 1374 AN: 4822

European-Finnish (FIN) AF: 0.364 AC: 3846 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20152 AN: 67972

Other (OTH) AF: 0.361 AC: 763 AN: 2114

Alfa AF: 0.366 Hom.: 3253

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6800768; hg19: chr3-24113252;