rs9270986

chr6-32606283-A-Cchr6-32606283-A-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 0.845 in 151,836 control chromosomes in the GnomAD database, including 54,306 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 0.85 (54306 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.869 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: 0.845 AC: 128237 AN: 151718 Hom.: 54262 Cov.: 30

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.845 AC: 128333 AN: 151836 Hom.: 54306 Cov.: 30 AF XY: 0.844 AC XY: 62641 AN XY: 74210

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.871

Alfa AF: 0.845 Hom.: 66621

Bravo AF: 0.850

Asia WGS AF: 0.746 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
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: rs9270986; hg19: chr6-32574060;