chr14-20445837-C-T

Variant names:

• chr14-20445837-C-T
• rs11160711
• ENST00000800201.1:n.367-1407C>T

Variant summary

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

The ENST00000800201.1(ENSG00000291038):​n.367-1407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,996 control chromosomes in the GnomAD database, including 7,514 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 0.31 (7514 hom., cov: 32)
• Consequence: ENSG00000291038 ENST00000800201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 15 publications found

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 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
ENSG00000291038	ENST00000800201.1	n.367-1407C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46944 AN: 151878 Hom.: 7514 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.309 AC: 46959 AN: 151996 Hom.: 7514 Cov.: 32 AF XY: 0.314 AC XY: 23298 AN XY: 74298

African (AFR) AF: 0.271 AC: 11222 AN: 41440

American (AMR) AF: 0.240 AC: 3672 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1814 AN: 5164

South Asian (SAS) AF: 0.391 AC: 1879 AN: 4810

European-Finnish (FIN) AF: 0.407 AC: 4290 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21362 AN: 67966

Other (OTH) AF: 0.334 AC: 706 AN: 2116

Alfa AF: 0.314 Hom.: 12593

Bravo AF: 0.293

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.81
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11160711; hg19: chr14-20913996;