rs2798983

Variant names:

• chr14-41303030-C-T
• rs2798983

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 0.756 in 151,532 control chromosomes in the GnomAD database, including 43,542 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 0.76 (43542 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=9.289).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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: 0.756 AC: 114458 AN: 151414 Hom.: 43483 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.756 AC: 114577 AN: 151532 Hom.: 43542 Cov.: 30 AF XY: 0.755 AC XY: 55926 AN XY: 74062

African (AFR) AF: 0.822 AC: 34053 AN: 41444

American (AMR) AF: 0.785 AC: 11907 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2667 AN: 3464

East Asian (EAS) AF: 0.750 AC: 3859 AN: 5144

South Asian (SAS) AF: 0.653 AC: 3145 AN: 4814

European-Finnish (FIN) AF: 0.683 AC: 7210 AN: 10552

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49210 AN: 67636

Other (OTH) AF: 0.777 AC: 1638 AN: 2108

Alfa AF: 0.758 Hom.: 5668

Bravo AF: 0.767

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	9.3
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs2798983; hg19: -;