rs1373900

Variant names:

• chr2-192871656-C-T
• rs1373900

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.513 AC: 21237 AN: 41408

American (AMR) AF: 0.377 AC: 5710 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1432 AN: 3452

East Asian (EAS) AF: 0.477 AC: 2443 AN: 5120

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4818

European-Finnish (FIN) AF: 0.352 AC: 3713 AN: 10554

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24857 AN: 67690

Other (OTH) AF: 0.434 AC: 910 AN: 2096

Alfa AF: 0.386 Hom.: 5588

Bravo AF: 0.417

Asia WGS AF: 0.515 AC: 1785 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	10
DANN	Benign	0.85
PhyloP100		0.0070

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1373900; hg19: chr2-193736382;