14-98083046-T-C

Variant names:

• chr14-98083046-T-C
• rs10782490
• ENST00000555776.1:n.122-2521A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555776.1(ENSG00000259097):​n.122-2521A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,590 control chromosomes in the GnomAD database, including 20,306 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 0.52 (20306 hom., cov: 30)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 4 publications found

Genes affected

ENSG00000259097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370655	XR_001750876.2	n.96-2521A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259097	ENST00000555776.1	n.122-2521A>G		intron_variant	Intron 1 of 2	4
ENSG00000259097	ENST00000663808.2	n.206-2521A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78268 AN: 151470 Hom.: 20268 Cov.: 30

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.517 AC: 78362 AN: 151590 Hom.: 20306 Cov.: 30 AF XY: 0.517 AC XY: 38258 AN XY: 74032

African (AFR) AF: 0.545 AC: 22525 AN: 41328

American (AMR) AF: 0.588 AC: 8950 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1652 AN: 3460

East Asian (EAS) AF: 0.541 AC: 2739 AN: 5062

South Asian (SAS) AF: 0.416 AC: 1997 AN: 4798

European-Finnish (FIN) AF: 0.518 AC: 5436 AN: 10490

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33390 AN: 67922

Other (OTH) AF: 0.543 AC: 1140 AN: 2100

Alfa AF: 0.504 Hom.: 53292

Bravo AF: 0.529

Asia WGS AF: 0.483 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs10782490; hg19: chr14-98549383;