chr14-42699522-T-A

Position:

• chr14-42699522-T-A

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-3583T>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 0.699 in 151,986 control chromosomes in the GnomAD database, including 37,756 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 0.70 (37756 hom., cov: 33)
• Consequence: ENST00000557251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000557251.1	n.167-3583T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106133 AN: 151868 Hom.: 37726 Cov.: 33

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.699 AC: 106217 AN: 151986 Hom.: 37756 Cov.: 33 AF XY: 0.699 AC XY: 51941 AN XY: 74312

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.723

Alfa AF: 0.739 Hom.: 5244

Bravo AF: 0.684

Asia WGS AF: 0.642 AC: 2213 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
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: rs1627270; hg19: chr14-43168725;