2-203745673-C-T

Variant names:

• chr2-203745673-C-T
• rs1980422

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 0.781 in 152,072 control chromosomes in the GnomAD database, including 46,536 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 0.78 (46536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603
• Publications: 92 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 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: 0.781 AC: 118737 AN: 151954 Hom.: 46505 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.781 AC: 118817 AN: 152072 Hom.: 46536 Cov.: 32 AF XY: 0.787 AC XY: 58516 AN XY: 74332

African (AFR) AF: 0.778 AC: 32260 AN: 41442

American (AMR) AF: 0.814 AC: 12443 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4675 AN: 5174

South Asian (SAS) AF: 0.912 AC: 4398 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8650 AN: 10578

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51555 AN: 67980

Other (OTH) AF: 0.762 AC: 1603 AN: 2104

Alfa AF: 0.772 Hom.: 75880

Bravo AF: 0.779

Asia WGS AF: 0.887 AC: 3069 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	15
DANN	Benign	0.78
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs1980422; hg19: chr2-204610396;