chr14-53917227-T-C

Variant names:

• chr14-53917227-T-C
• rs11157990
• ENST00000729148.1:n.188-315A>G

Variant summary

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

The ENST00000729148.1(ENSG00000295303):​n.188-315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,094 control chromosomes in the GnomAD database, including 4,714 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 0.24 (4714 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000295303 ENST00000729148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 7 publications found

Genes affected

ENSG00000295303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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
ENSG00000295303	ENST00000729148.1	n.188-315A>G		intron_variant	Intron 1 of 4
ENSG00000295303	ENST00000729149.1	n.141-315A>G		intron_variant	Intron 1 of 3
ENSG00000295303	ENST00000729150.1	n.138-315A>G		intron_variant	Intron 1 of 2
ENSG00000231922	ENST00000426913.1	n.*43A>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35812 AN: 151972 Hom.: 4719 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.251

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.235 AC: 35795 AN: 152094 Hom.: 4714 Cov.: 33 AF XY: 0.236 AC XY: 17535 AN XY: 74352

African (AFR) AF: 0.127 AC: 5273 AN: 41504

American (AMR) AF: 0.234 AC: 3578 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 965 AN: 3464

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5160

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4822

European-Finnish (FIN) AF: 0.270 AC: 2858 AN: 10576

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19434 AN: 67968

Other (OTH) AF: 0.248 AC: 524 AN: 2114

Alfa AF: 0.263 Hom.: 3485

Bravo AF: 0.227

Asia WGS AF: 0.229 AC: 796 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs11157990; hg19: chr14-54383945;