3-172457284-G-C

Variant names:

• chr3-172457284-G-C
• rs490683

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 0.278 in 151,918 control chromosomes in the GnomAD database, including 6,068 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 0.28 (6068 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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: 0.278 AC: 42248 AN: 151802 Hom.: 6063 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.278 AC: 42289 AN: 151918 Hom.: 6068 Cov.: 31 AF XY: 0.279 AC XY: 20740 AN XY: 74250

African (AFR) AF: 0.264 AC: 10933 AN: 41418

American (AMR) AF: 0.314 AC: 4792 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1927 AN: 5140

South Asian (SAS) AF: 0.220 AC: 1056 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3116 AN: 10554

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19079 AN: 67962

Other (OTH) AF: 0.256 AC: 539 AN: 2108

Alfa AF: 0.147 Hom.: 257

Bravo AF: 0.285

Asia WGS AF: 0.283 AC: 989 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	0.32
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs490683; hg19: chr3-172175074;