3-74669607-T-C

Variant names:

• chr3-74669607-T-C
• rs1447826

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 0.517 in 151,364 control chromosomes in the GnomAD database, including 21,219 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 0.52 (21219 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 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: 0.518 AC: 78288 AN: 151244 Hom.: 21222 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.517 AC: 78296 AN: 151364 Hom.: 21219 Cov.: 31 AF XY: 0.519 AC XY: 38406 AN XY: 73930

African (AFR) AF: 0.388 AC: 16037 AN: 41340

American (AMR) AF: 0.542 AC: 8206 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2227 AN: 3460

East Asian (EAS) AF: 0.258 AC: 1310 AN: 5074

South Asian (SAS) AF: 0.493 AC: 2371 AN: 4806

European-Finnish (FIN) AF: 0.606 AC: 6381 AN: 10534

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.589 AC: 39850 AN: 67700

Other (OTH) AF: 0.517 AC: 1087 AN: 2102

Alfa AF: 0.802 Hom.: 15182

Bravo AF: 0.504

Asia WGS AF: 0.372 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.1
DANN	Benign	0.87
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1447826; hg19: chr3-74718758;