rs2469798

Variant names:

• chr17-3258986-T-C
• rs2469798

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 0.594 in 152,090 control chromosomes in the GnomAD database, including 29,150 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 0.59 (29150 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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: 0.594 AC: 90285 AN: 151972 Hom.: 29112 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.0726

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.594 AC: 90371 AN: 152090 Hom.: 29150 Cov.: 31 AF XY: 0.583 AC XY: 43365 AN XY: 74352

African (AFR) AF: 0.834 AC: 34588 AN: 41496

American (AMR) AF: 0.498 AC: 7616 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3470

East Asian (EAS) AF: 0.0722 AC: 374 AN: 5180

South Asian (SAS) AF: 0.504 AC: 2425 AN: 4814

European-Finnish (FIN) AF: 0.429 AC: 4531 AN: 10564

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37073 AN: 67968

Other (OTH) AF: 0.568 AC: 1198 AN: 2108

Alfa AF: 0.553 Hom.: 22521

Bravo AF: 0.606

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.77
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs2469798; hg19: chr17-3162280;