chr14-38108596-T-G

Variant names:

• chr14-38108596-T-G
• rs10498337
• ENST00000554687.1:n.200+59744A>C

Variant summary

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

The ENST00000554687.1(ENSG00000259048):​n.200+59744A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,164 control chromosomes in the GnomAD database, including 2,030 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 0.16 (2030 hom., cov: 32)
• Consequence: ENSG00000259048 ENST00000554687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775
• Publications: 4 publications found

Genes affected

ENSG00000259048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554687.1. 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
	ENSG00000259048	ENST00000554687.1	TSL:4	n.200+59744A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23737 AN: 152046 Hom.: 2030 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.156 AC: 23729 AN: 152164 Hom.: 2030 Cov.: 32 AF XY: 0.153 AC XY: 11391 AN XY: 74388

African (AFR) AF: 0.120 AC: 5000 AN: 41538

American (AMR) AF: 0.146 AC: 2225 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3472

East Asian (EAS) AF: 0.0662 AC: 343 AN: 5184

South Asian (SAS) AF: 0.108 AC: 521 AN: 4822

European-Finnish (FIN) AF: 0.138 AC: 1466 AN: 10594

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12762 AN: 67966

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.171 Hom.: 3599

Bravo AF: 0.155

Asia WGS AF: 0.102 AC: 355 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.4
DANN	Benign	0.88
PhyloP100		0.78

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: rs10498337;

hg19: chr14-38577801;