chr3-74693474-T-A

Variant names:

• chr3-74693474-T-A
• rs6762970

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 0.321 in 151,826 control chromosomes in the GnomAD database, including 9,626 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 0.32 (9626 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.321 AC: 48701 AN: 151708 Hom.: 9630 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.321 AC: 48689 AN: 151826 Hom.: 9626 Cov.: 31 AF XY: 0.320 AC XY: 23759 AN XY: 74162

African (AFR) AF: 0.130 AC: 5402 AN: 41450

American (AMR) AF: 0.292 AC: 4450 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1548 AN: 3470

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1260 AN: 4796

European-Finnish (FIN) AF: 0.498 AC: 5230 AN: 10494

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29551 AN: 67906

Other (OTH) AF: 0.321 AC: 677 AN: 2110

Alfa AF: 0.375 Hom.: 1480

Bravo AF: 0.296

Asia WGS AF: 0.143 AC: 499 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	2.4
DANN	Benign	0.46
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6762970; hg19: chr3-74742625;