chr3-1674807-T-C

Position:

• chr3-1674807-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 0.256 in 152,042 control chromosomes in the GnomAD database, including 5,762 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 0.26 (5762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38956 AN: 151926 Hom.: 5749 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.256 AC: 38997 AN: 152042 Hom.: 5762 Cov.: 32 AF XY: 0.259 AC XY: 19224 AN XY: 74324

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.253

Alfa AF: 0.237 Hom.: 850

Bravo AF: 0.258

Asia WGS AF: 0.438 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6790607; hg19: chr3-1716491;