ENST00000555776.1:n.121+28788G>A

Variant names:

• chr14-98176235-C-T
• rs10484128
• ENST00000555776.1:n.121+28788G>A

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.121+28788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,156 control chromosomes in the GnomAD database, including 1,027 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 0.11 (1027 hom., cov: 31)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259097	ENST00000555776.1	TSL:4	n.121+28788G>A		intron	N/A
	ENSG00000259097	ENST00000733052.1		n.121-13130G>A		intron	N/A
	ENSG00000259097	ENST00000733053.1		n.113-13127G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16671 AN: 152038 Hom.: 1028 Cov.: 31

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.110 AC: 16673 AN: 152156 Hom.: 1027 Cov.: 31 AF XY: 0.106 AC XY: 7919 AN XY: 74404

African (AFR) AF: 0.0594 AC: 2467 AN: 41508

American (AMR) AF: 0.114 AC: 1738 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3470

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5180

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4820

European-Finnish (FIN) AF: 0.0959 AC: 1017 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10087 AN: 67976

Other (OTH) AF: 0.142 AC: 300 AN: 2108

Alfa AF: 0.133 Hom.: 4679

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10484128; hg19: chr14-98642572;