chr6-31081878-G-A

Variant names:

• chr6-31081878-G-A
• rs9380215

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 0.0674 in 152,124 control chromosomes in the GnomAD database, including 496 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 0.067 (496 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.0676 AC: 10272 AN: 152006 Hom.: 501 Cov.: 30

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0674 AC: 10255 AN: 152124 Hom.: 496 Cov.: 30 AF XY: 0.0698 AC XY: 5192 AN XY: 74358

African (AFR) AF: 0.0248 AC: 1031 AN: 41524

American (AMR) AF: 0.0902 AC: 1377 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5162

South Asian (SAS) AF: 0.131 AC: 629 AN: 4816

European-Finnish (FIN) AF: 0.0848 AC: 896 AN: 10568

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0722 AC: 4909 AN: 68004

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0710 Hom.: 1238

Bravo AF: 0.0647

Asia WGS AF: 0.135 AC: 471 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	2.9
DANN	Benign	0.53
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs9380215; hg19: chr6-31049655;