chr14-29435220-C-T

Variant names:

• chr14-29435220-C-T
• rs11161057
• ENST00000549515.2:n.468-957C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000549515.2(ENSG00000258107):​n.468-957C>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 ENST00000549515.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 1 publications found

Genes affected

ENSG00000258107 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549515.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258107	ENST00000549515.2	TSL:2	n.468-957C>T		intron	N/A
	ENSG00000258107	ENST00000649245.2		n.590-957C>T		intron	N/A
	ENSG00000286040	ENST00000652296.1		n.369-6404G>A		intron	N/A

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

African (AFR) AF: 0.300 AC: 12408 AN: 41392

American (AMR) AF: 0.390 AC: 5962 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5166

South Asian (SAS) AF: 0.207 AC: 992 AN: 4800

European-Finnish (FIN) AF: 0.427 AC: 4493 AN: 10518

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30287 AN: 67952

Other (OTH) AF: 0.398 AC: 838 AN: 2106

Alfa AF: 0.362 Hom.: 3863

Bravo AF: 0.382

Asia WGS AF: 0.196 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.7
DANN	Benign	0.47
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs11161057; hg19: chr14-29904426;