rs3132451

Positions:

• chr6-31614248-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 0.175 in 152,214 control chromosomes in the GnomAD database, including 2,562 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 0.18 (2562 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31614248G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26675 AN: 152096 Hom.: 2562 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.175 AC: 26674 AN: 152214 Hom.: 2562 Cov.: 32 AF XY: 0.170 AC XY: 12658 AN XY: 74418

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0792

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.151

Alfa AF: 0.194 Hom.: 1720

Bravo AF: 0.173

Asia WGS AF: 0.0950 AC: 331 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	2.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132451; hg19: chr6-31582025;