chr6-31353550-A-G

Position:

• chr6-31353550-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 0.295 in 152,100 control chromosomes in the GnomAD database, including 6,899 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 0.30 (6899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44834 AN: 151982 Hom.: 6881 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.295 AC: 44880 AN: 152100 Hom.: 6899 Cov.: 32 AF XY: 0.304 AC XY: 22589 AN XY: 74358

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.313

Alfa AF: 0.262 Hom.: 843

Bravo AF: 0.291

Asia WGS AF: 0.342 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9266095; hg19: chr6-31321327;