rs935367

Variant names:

• chr2-192274716-G-A
• rs935367

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 0.797 in 152,140 control chromosomes in the GnomAD database, including 48,572 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 0.80 (48572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.797 AC: 121158 AN: 152022 Hom.: 48538 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.797 AC: 121248 AN: 152140 Hom.: 48572 Cov.: 32 AF XY: 0.795 AC XY: 59102 AN XY: 74372

African (AFR) AF: 0.824 AC: 34189 AN: 41498

American (AMR) AF: 0.756 AC: 11558 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2747 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2563 AN: 5156

South Asian (SAS) AF: 0.803 AC: 3872 AN: 4820

European-Finnish (FIN) AF: 0.792 AC: 8381 AN: 10584

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55278 AN: 68006

Other (OTH) AF: 0.773 AC: 1635 AN: 2114

Alfa AF: 0.811 Hom.: 7475

Bravo AF: 0.788

Asia WGS AF: 0.712 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.33
DANN	Benign	0.73
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs935367; hg19: chr2-193139442;