rs935367

chr2-192274716-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;