6-31523223-A-G

Position:

• chr6-31523223-A-G

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 0.792 in 152,146 control chromosomes in the GnomAD database, including 47,798 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 0.79 (47798 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31523223A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120352 AN: 152028 Hom.: 47757 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.792 AC: 120446 AN: 152146 Hom.: 47798 Cov.: 31 AF XY: 0.797 AC XY: 59303 AN XY: 74370

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.789

Alfa AF: 0.767 Hom.: 28469

Bravo AF: 0.793

Asia WGS AF: 0.823 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095227; hg19: chr6-31491000;