rs7932938

Positions:

• chr11-18793748-T-G

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 0.469 in 152,028 control chromosomes in the GnomAD database, including 17,230 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 0.47 (17230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 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: 0.469 AC: 71253 AN: 151910 Hom.: 17235 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.469 AC: 71269 AN: 152028 Hom.: 17230 Cov.: 32 AF XY: 0.467 AC XY: 34679 AN XY: 74312

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.443

Alfa AF: 0.506 Hom.: 39176

Bravo AF: 0.460

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7932938; hg19: chr11-18815295;