rs7151526

Variant names:

• chr14-94397299-C-A
• rs7151526
• ENST00000693506.1:n.124+6405C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000693506.1(ENSG00000256357):​n.124+6405C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0338 in 152,278 control chromosomes in the GnomAD database, including 135 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 0.034 (135 hom., cov: 33)
• Consequence: ENSG00000256357 ENST00000693506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 28 publications found

Genes affected

ENSG00000256357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0338 (5143/152278) while in subpopulation NFE AF = 0.0498 (3385/68024). AF 95% confidence interval is 0.0484. There are 135 homozygotes in GnomAd4. There are 2524 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 135 gene

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
ENSG00000256357	ENST00000693506.1	n.124+6405C>A		intron_variant	Intron 1 of 1
ENSG00000256357	ENST00000811346.1	n.227+7434C>A		intron_variant	Intron 1 of 2
ENSG00000256357	ENST00000811347.1	n.208+7434C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5144 AN: 152160 Hom.: 136 Cov.: 33

Gnomad AFR AF: 0.00859

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0338 AC: 5143 AN: 152278 Hom.: 135 Cov.: 33 AF XY: 0.0339 AC XY: 2524 AN XY: 74454

African (AFR) AF: 0.00857 AC: 356 AN: 41550

American (AMR) AF: 0.0348 AC: 533 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0379 AC: 183 AN: 4824

European-Finnish (FIN) AF: 0.0387 AC: 410 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0498 AC: 3385 AN: 68024

Other (OTH) AF: 0.0355 AC: 75 AN: 2114

Alfa AF: 0.0430 Hom.: 297

Bravo AF: 0.0324

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.23
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7151526; hg19: chr14-94863636;