6-31384336-T-C

Variant names:

• chr6-31384336-T-C
• rs9266772

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 0.183 in 151,756 control chromosomes in the GnomAD database, including 2,850 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 (2850 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

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 (AMR) allele frequency at 95% confidence interval = 0.244 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: 0.183 AC: 27688 AN: 151638 Hom.: 2847 Cov.: 30

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0889

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.183 AC: 27715 AN: 151756 Hom.: 2850 Cov.: 30 AF XY: 0.179 AC XY: 13243 AN XY: 74180

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0895

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.215

Alfa AF: 0.186 Hom.: 1591

Bravo AF: 0.196

Asia WGS AF: 0.185 AC: 644 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	8.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9266772; hg19: chr6-31352113;