rs7151526

chr14-94397299-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000693506.1(ENSG00000289541):n.124+6405C>A variant causes a intron, non coding transcript 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: ENST00000693506.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 136 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000693506.1	n.124+6405C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00857

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.0387

Gnomad4 NFE AF: 0.0498

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0390 Hom.: 33

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7151526; hg19: chr14-94863636;