rs7930778

Variant names:

• chr11-58268884-T-C
• rs7930778

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 0.657 in 152,096 control chromosomes in the GnomAD database, including 33,660 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 0.66 (33660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 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: 0.657 AC: 99871 AN: 151978 Hom.: 33614 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.657 AC: 99972 AN: 152096 Hom.: 33660 Cov.: 32 AF XY: 0.662 AC XY: 49166 AN XY: 74320

African (AFR) AF: 0.791 AC: 32846 AN: 41526

American (AMR) AF: 0.697 AC: 10650 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3472

East Asian (EAS) AF: 0.853 AC: 4406 AN: 5166

South Asian (SAS) AF: 0.669 AC: 3228 AN: 4824

European-Finnish (FIN) AF: 0.601 AC: 6338 AN: 10554

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38351 AN: 67968

Other (OTH) AF: 0.666 AC: 1405 AN: 2110

Alfa AF: 0.597 Hom.: 14074

Bravo AF: 0.673

Asia WGS AF: 0.730 AC: 2536 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.029
DANN	Benign	0.24
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7930778; hg19: chr11-58036356;