3-174375870-T-C

Variant names:

• chr3-174375870-T-C
• rs7628369

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 0.674 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.850 AC: 35229 AN: 41442

American (AMR) AF: 0.660 AC: 10072 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3832 AN: 5146

South Asian (SAS) AF: 0.650 AC: 3132 AN: 4820

European-Finnish (FIN) AF: 0.637 AC: 6712 AN: 10534

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39295 AN: 67944

Other (OTH) AF: 0.646 AC: 1366 AN: 2114

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7628369; hg19: chr3-174093660;