rs9348756

chr6-27260480-G-Achr6-27260480-G-C

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 0.0653 in 152,154 control chromosomes in the GnomAD database, including 582 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 0.065 (582 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0833 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: 0.0653 AC: 9934 AN: 152036 Hom.: 583 Cov.: 31

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0653 AC: 9932 AN: 152154 Hom.: 582 Cov.: 31 AF XY: 0.0697 AC XY: 5187 AN XY: 74380

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.0239

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0377 Hom.: 33

Bravo AF: 0.0504

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9348756; hg19: chr6-27228259;