rs9282626

Variant names:

• chr11-34437971-T-C
• rs9282626

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0627 AC: 2608 AN: 41562

American (AMR) AF: 0.0331 AC: 506 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.0242 AC: 117 AN: 4828

European-Finnish (FIN) AF: 0.0208 AC: 221 AN: 10618

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2961 AN: 68016

Other (OTH) AF: 0.0526 AC: 111 AN: 2112

Alfa AF: 0.0453 Hom.: 119

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
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs9282626; hg19: chr11-34459518;