rs9268560

Positions:

• chr6-32421735-C-G
• chr6-32421735-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 0.555 in 151,972 control chromosomes in the GnomAD database, including 23,599 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 0.55 (23599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.603 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: 0.555 AC: 84238 AN: 151854 Hom.: 23577 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.555 AC: 84298 AN: 151972 Hom.: 23599 Cov.: 31 AF XY: 0.558 AC XY: 41458 AN XY: 74274

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.592

Alfa AF: 0.425 Hom.: 1206

Bravo AF: 0.561

Asia WGS AF: 0.559 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268560; hg19: chr6-32389512;