14-29435220-C-T

Variant names:

• chr14-29435220-C-T
• rs11161057
• ENST00000549515.1:n.412-957C>T

Variant summary

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

The ENST00000549515.1(ENSG00000258107):​n.412-957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,886 control chromosomes in the GnomAD database, including 11,583 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 0.38 (11583 hom., cov: 32)
• Consequence: ENSG00000258107 ENST00000549515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

Genes affected

ENSG00000258107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

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
ENSG00000258107	ENST00000549515.1	n.412-957C>T		intron_variant	Intron 3 of 3	2
ENSG00000258107	ENST00000649245.1	n.566-957C>T		intron_variant	Intron 2 of 2
ENSG00000286040	ENST00000652296.1	n.369-6404G>A		intron_variant	Intron 3 of 4
ENSG00000258107	ENST00000667982.1	n.196-957C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58140 AN: 151766 Hom.: 11587 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.383 AC: 58171 AN: 151886 Hom.: 11583 Cov.: 32 AF XY: 0.376 AC XY: 27942 AN XY: 74238

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.398

Alfa AF: 0.340 Hom.: 1826

Bravo AF: 0.382

Asia WGS AF: 0.196 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11161057; hg19: chr14-29904426;