rs9276615

Positions:

• chr6-32775440-C-T

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 0.705 in 151,744 control chromosomes in the GnomAD database, including 37,806 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 0.70 (37806 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106859 AN: 151626 Hom.: 37788 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.705 AC: 106919 AN: 151744 Hom.: 37806 Cov.: 31 AF XY: 0.710 AC XY: 52676 AN XY: 74168

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.708

Alfa AF: 0.702 Hom.: 23866

Bravo AF: 0.693

Asia WGS AF: 0.800 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9276615; hg19: chr6-32743217;