ENST00000555776.1:n.122-35797C>A

Variant names:

• chr14-98116322-G-T
• rs17773233
• ENST00000555776.1:n.122-35797C>A

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-35797C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,074 control chromosomes in the GnomAD database, including 2,288 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 (2288 hom., cov: 31)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370655	XR_001750876.2	n.96-35797C>A		intron_variant	Intron 1 of 3
LOC105370653	XR_944188.3	n.481-202G>T		intron_variant	Intron 4 of 4
LOC105370653	XR_944189.3	n.478-202G>T		intron_variant	Intron 4 of 4
LOC105370653	XR_944190.3	n.339-202G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259097	ENST00000555776.1	n.122-35797C>A		intron_variant	Intron 1 of 2	4
ENSG00000307462	ENST00000826440.1	n.319-202G>T		intron_variant	Intron 3 of 3
ENSG00000307462	ENST00000826441.1	n.446-202G>T		intron_variant	Intron 4 of 4
ENSG00000307462	ENST00000826442.1	n.226-202G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24151 AN: 151954 Hom.: 2285 Cov.: 31

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.159 AC: 24164 AN: 152074 Hom.: 2288 Cov.: 31 AF XY: 0.156 AC XY: 11572 AN XY: 74312

African (AFR) AF: 0.0740 AC: 3071 AN: 41490

American (AMR) AF: 0.153 AC: 2346 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.0870 AC: 449 AN: 5162

South Asian (SAS) AF: 0.108 AC: 522 AN: 4816

European-Finnish (FIN) AF: 0.176 AC: 1854 AN: 10550

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

European-Non Finnish (NFE) AF: 0.216 AC: 14706 AN: 67972

Other (OTH) AF: 0.158 AC: 335 AN: 2114

Alfa AF: 0.172 Hom.: 314

Bravo AF: 0.155

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.77
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17773233; hg19: chr14-98582659;