2-200848731-T-C

Variant names:

• chr2-200848731-T-C
• rs4674520

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 0.798 in 151,308 control chromosomes in the GnomAD database, including 48,300 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 0.80 (48300 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.798 AC: 120590 AN: 151198 Hom.: 48266 Cov.: 28

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.798 AC: 120686 AN: 151308 Hom.: 48300 Cov.: 28 AF XY: 0.790 AC XY: 58363 AN XY: 73896

African (AFR) AF: 0.841 AC: 34729 AN: 41302

American (AMR) AF: 0.761 AC: 11549 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2684 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3098 AN: 5116

South Asian (SAS) AF: 0.573 AC: 2723 AN: 4754

European-Finnish (FIN) AF: 0.792 AC: 8197 AN: 10352

Middle Eastern (MID) AF: 0.690 AC: 196 AN: 284

European-Non Finnish (NFE) AF: 0.812 AC: 55115 AN: 67864

Other (OTH) AF: 0.791 AC: 1651 AN: 2088

Alfa AF: 0.791 Hom.: 31301

Bravo AF: 0.800

Asia WGS AF: 0.582 AC: 2024 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs4674520; hg19: chr2-201713454;