3-174375870-T-C

Position:

• chr3-174375870-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 0.674 in 151,934 control chromosomes in the GnomAD database, including 35,548 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 0.67 (35548 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 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: 0.673 AC: 102247 AN: 151816 Hom.: 35499 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.674 AC: 102362 AN: 151934 Hom.: 35548 Cov.: 31 AF XY: 0.676 AC XY: 50206 AN XY: 74246

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.646

Alfa AF: 0.640 Hom.: 3980

Bravo AF: 0.682

Asia WGS AF: 0.704 AC: 2446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628369; hg19: chr3-174093660;