rs1378753

chr2-137794360-T-Achr2-137794360-T-Cchr2-137794360-T-G

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 0.82 in 151,914 control chromosomes in the GnomAD database, including 52,704 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 0.82 (52704 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.820 AC: 124483 AN: 151798 Hom.: 52672 Cov.: 30

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.820 AC: 124563 AN: 151914 Hom.: 52704 Cov.: 30 AF XY: 0.817 AC XY: 60692 AN XY: 74246

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.805

Alfa AF: 0.868 Hom.: 3501

Bravo AF: 0.792

Asia WGS AF: 0.645 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.033
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378753; hg19: chr2-138551930;