rs7933280

Variant names:

• chr11-18250382-T-G
• rs7933280

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 0.145 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.421 AC: 17438 AN: 41460

American (AMR) AF: 0.0691 AC: 1057 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3470

East Asian (EAS) AF: 0.0654 AC: 339 AN: 5180

South Asian (SAS) AF: 0.144 AC: 693 AN: 4822

European-Finnish (FIN) AF: 0.00461 AC: 49 AN: 10620

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0306 AC: 2081 AN: 68010

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.0693 Hom.: 2987

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs7933280; hg19: chr11-18271929;