rs935367

Variant names:

• chr2-192274716-G-A
• rs935367

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 0.797 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.797 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

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.773

Alfa AF: 0.812 Hom.: 7236

Bravo AF: 0.788

Asia WGS AF: 0.712 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.33
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: rs935367; hg19: chr2-193139442;