rs332759

Variant names:

• chr11-98768944-C-T
• rs332759

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 0.323 in 152,032 control chromosomes in the GnomAD database, including 9,171 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 0.32 (9171 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.323 AC: 49130 AN: 151914 Hom.: 9168 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.323 AC: 49146 AN: 152032 Hom.: 9171 Cov.: 32 AF XY: 0.323 AC XY: 24001 AN XY: 74322

African (AFR) AF: 0.150 AC: 6225 AN: 41474

American (AMR) AF: 0.438 AC: 6690 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3470

East Asian (EAS) AF: 0.118 AC: 611 AN: 5178

South Asian (SAS) AF: 0.397 AC: 1912 AN: 4822

European-Finnish (FIN) AF: 0.319 AC: 3365 AN: 10550

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27590 AN: 67950

Other (OTH) AF: 0.389 AC: 822 AN: 2114

Alfa AF: 0.396 Hom.: 20117

Bravo AF: 0.323

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.76
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs332759; hg19: chr11-98639674;