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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555776.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259097	ENST00000555776.1	TSL:4	n.122-2521A>G		intron	N/A
	ENSG00000259097	ENST00000663808.2		n.206-2521A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10782490;

hg19: chr14-98549383;