rs17127526

Variant names:

• chr14-54391243-G-A
• rs17127526
• ENST00000770016.1:n.126-2309C>T

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.126-2309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 152,160 control chromosomes in the GnomAD database, including 564 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 0.069 (564 hom., cov: 31)
• Consequence: ENSG00000300202 ENST00000770016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 1 publications found

Genes affected

ENSG00000300202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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
ENSG00000300202	ENST00000770016.1	n.126-2309C>T		intron_variant	Intron 1 of 3
ENSG00000300202	ENST00000770017.1	n.252+1084C>T		intron_variant	Intron 1 of 2
ENSG00000300202	ENST00000770018.1	n.245+1084C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10543 AN: 152042 Hom.: 566 Cov.: 31

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0692 AC: 10537 AN: 152160 Hom.: 564 Cov.: 31 AF XY: 0.0711 AC XY: 5290 AN XY: 74384

African (AFR) AF: 0.0707 AC: 2934 AN: 41500

American (AMR) AF: 0.0531 AC: 812 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5170

South Asian (SAS) AF: 0.189 AC: 910 AN: 4810

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10606

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0545 AC: 3704 AN: 68010

Other (OTH) AF: 0.0867 AC: 183 AN: 2110

Alfa AF: 0.0630 Hom.: 564

Bravo AF: 0.0701

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs17127526; hg19: chr14-54857961;