rs7935378

Variant names:

• chr11-102519090-T-C
• rs7935378

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 0.228 in 152,166 control chromosomes in the GnomAD database, including 4,635 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 0.23 (4635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34561 AN: 152048 Hom.: 4617 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.228 AC: 34633 AN: 152166 Hom.: 4635 Cov.: 32 AF XY: 0.225 AC XY: 16743 AN XY: 74412

African (AFR) AF: 0.368 AC: 15278 AN: 41492

American (AMR) AF: 0.242 AC: 3699 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1304 AN: 5176

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10608

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10679 AN: 67986

Other (OTH) AF: 0.239 AC: 505 AN: 2110

Alfa AF: 0.174 Hom.: 2473

Bravo AF: 0.242

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7935378; hg19: chr11-102389821;