rs1026504

Variant names:

• chr14-98363668-A-C
• rs1026504

Your query was ambiguous. Multiple possible variants found:

• chr14-98363668-A-C
• chr14-98363668-A-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 0.462 in 152,044 control chromosomes in the GnomAD database, including 16,500 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 0.46 (16500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.462 AC: 70213 AN: 151926 Hom.: 16466 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.462 AC: 70297 AN: 152044 Hom.: 16500 Cov.: 32 AF XY: 0.458 AC XY: 33999 AN XY: 74308

African (AFR) AF: 0.475 AC: 19681 AN: 41474

American (AMR) AF: 0.386 AC: 5894 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2226 AN: 5160

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4824

European-Finnish (FIN) AF: 0.454 AC: 4794 AN: 10570

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32925 AN: 67972

Other (OTH) AF: 0.443 AC: 934 AN: 2106

Alfa AF: 0.473 Hom.: 54057

Bravo AF: 0.458

Asia WGS AF: 0.390 AC: 1357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1026504; hg19: chr14-98830005;