rs7933280

chr11-18250382-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 0.145 in 152,184 control chromosomes in the GnomAD database, including 3,873 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 0.14 (3873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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: 0.145 AC: 21979 AN: 152066 Hom.: 3854 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.00461

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.145 AC: 22046 AN: 152184 Hom.: 3873 Cov.: 32 AF XY: 0.142 AC XY: 10548 AN XY: 74428

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.00461

Gnomad4 NFE AF: 0.0306

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0478 Hom.: 945

Bravo AF: 0.160

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.1
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7933280; hg19: chr11-18271929;