3-172457284-G-C

Position:

• chr3-172457284-G-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 0.278 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.172457284G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.256

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490683; hg19: chr3-172175074;