rs17112354

chr14-27186573-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656336.1(ENSG00000258081):n.550-19264C>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 0.0696 in 151,788 control chromosomes in the GnomAD database, including 520 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 0.070 (520 hom., cov: 32)
• Consequence: ENST00000656336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370420	XR_943662.3	n.265-19264C>A		intron_variant, non_coding_transcript_variant
LOC105370420	XR_001750686.2	n.133-19264C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656336.1	n.550-19264C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10562 AN: 151670 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0696 AC: 10559 AN: 151788 Hom.: 520 Cov.: 32 AF XY: 0.0732 AC XY: 5429 AN XY: 74186

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0673

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0769

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0765 Hom.: 677

Bravo AF: 0.0654

Asia WGS AF: 0.174 AC: 602 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.8
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17112354; hg19: chr14-27655779;