chr14-76514762-T-C

Variant names:

• chr14-76514762-T-C
• rs17583842
• ENST00000554926.1:n.311-12502A>G

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.311-12502A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,150 control chromosomes in the GnomAD database, including 3,086 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 0.18 (3086 hom., cov: 31)
• Consequence: ENSG00000259124 ENST00000554926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 10 publications found

Genes affected

ENSG00000259124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 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
ENSG00000259124	ENST00000554926.1	n.311-12502A>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27334 AN: 152032 Hom.: 3089 Cov.: 31

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.180 AC: 27320 AN: 152150 Hom.: 3086 Cov.: 31 AF XY: 0.179 AC XY: 13312 AN XY: 74380

African (AFR) AF: 0.0465 AC: 1930 AN: 41540

American (AMR) AF: 0.173 AC: 2642 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3470

East Asian (EAS) AF: 0.0938 AC: 485 AN: 5170

South Asian (SAS) AF: 0.164 AC: 787 AN: 4802

European-Finnish (FIN) AF: 0.252 AC: 2666 AN: 10576

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17142 AN: 67984

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.232 Hom.: 7393

Bravo AF: 0.167

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs17583842; hg19: chr14-76981105;