rs2498786

Variant names:

• chr14-104796031-C-G
• rs2498786

Your query was ambiguous. Multiple possible variants found:

• chr14-104796031-C-G
• chr14-104796031-C-T

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 0.498 in 151,996 control chromosomes in the GnomAD database, including 20,385 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 0.50 (20385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 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: 0.498 AC: 75628 AN: 151876 Hom.: 20375 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.498 AC: 75657 AN: 151996 Hom.: 20385 Cov.: 32 AF XY: 0.495 AC XY: 36803 AN XY: 74280

African (AFR) AF: 0.309 AC: 12831 AN: 41496

American (AMR) AF: 0.509 AC: 7774 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1080 AN: 5146

South Asian (SAS) AF: 0.409 AC: 1971 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6572 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41456 AN: 67928

Other (OTH) AF: 0.522 AC: 1102 AN: 2110

Alfa AF: 0.446 Hom.: 1418

Bravo AF: 0.481

Asia WGS AF: 0.311 AC: 1085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.4
DANN	Benign	0.56
PhyloP100		1.7
PromoterAI		0.0079	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2498786; hg19: chr14-105262368;