rs17583842

chr14-76514762-T-C

Variant summary

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

The ENST00000554926.1(ENSG00000259124):n.311-12502A>G 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 0.18 in 152,150 control chromosomes in the GnomAD database, including 3,086 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 0.18 (3086 hom., cov: 31)
• Consequence: ENST00000554926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554926.1	n.311-12502A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27334 AN: 152032 Hom.: 3089 Cov.: 31

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.180 AC: 27320 AN: 152150 Hom.: 3086 Cov.: 31 AF XY: 0.179 AC XY: 13312 AN XY: 74380

Gnomad4 AFR AF: 0.0465

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.0938

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.208

Alfa AF: 0.239 Hom.: 6123

Bravo AF: 0.167

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.9
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17583842; hg19: chr14-76981105;