3-74669607-T-C

Variant names:

• chr3-74669607-T-C
• rs1447826

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 0.517 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.517

Alfa AF: 0.765 Hom.: 11254

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447826; hg19: chr3-74718758;