rs9267546

chr6-31705659-G-A

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 0.142 in 152,202 control chromosomes in the GnomAD database, including 1,942 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 0.14 (1942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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: 0.142 AC: 21665 AN: 152084 Hom.: 1941 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0934

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.142 AC: 21676 AN: 152202 Hom.: 1942 Cov.: 32 AF XY: 0.140 AC XY: 10437 AN XY: 74426

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.162

Alfa AF: 0.104 Hom.: 1301

Bravo AF: 0.151

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267546; hg19: chr6-31673436;