rs332759

chr11-98768944-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 0.323 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.389

Alfa AF: 0.404 Hom.: 16290

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs332759; hg19: chr11-98639674;