rs9282626

Positions:

• chr11-34437971-T-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 0.0453 in 152,300 control chromosomes in the GnomAD database, including 164 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 0.045 (164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0607 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: 0.0452 AC: 6882 AN: 152184 Hom.: 163 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0453 AC: 6901 AN: 152300 Hom.: 164 Cov.: 32 AF XY: 0.0432 AC XY: 3220 AN XY: 74490

Gnomad4 AFR AF: 0.0627

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0448 Hom.: 105

Bravo AF: 0.0472

Asia WGS AF: 0.0160 AC: 55 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9282626; hg19: chr11-34459518;