rs1373900

Variant names:

• chr2-192871656-C-T
• rs1373900

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.415 in 151,486 control chromosomes in the GnomAD database, including 13,395 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 0.41 (13395 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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: 0.414 AC: 62742 AN: 151368 Hom.: 13380 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.415 AC: 62798 AN: 151486 Hom.: 13395 Cov.: 33 AF XY: 0.412 AC XY: 30508 AN XY: 74008

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.434

Alfa AF: 0.385 Hom.: 5474

Bravo AF: 0.417

Asia WGS AF: 0.515 AC: 1785 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	10
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373900; hg19: chr2-193736382;