rs1378753

Variant names:

• chr2-137794360-T-A
• rs1378753

Your query was ambiguous. Multiple possible variants found:

• chr2-137794360-T-A
• chr2-137794360-T-C
• chr2-137794360-T-G

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 0.82 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.653 AC: 26979 AN: 41336

American (AMR) AF: 0.757 AC: 11556 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3022 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2254 AN: 5160

South Asian (SAS) AF: 0.783 AC: 3770 AN: 4816

European-Finnish (FIN) AF: 0.959 AC: 10134 AN: 10572

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64039 AN: 67988

Other (OTH) AF: 0.805 AC: 1696 AN: 2108

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1378753; hg19: chr2-138551930;