chr14-54912497-T-A

Variant names:

• chr14-54912497-T-A
• rs8008858
• ENST00000809739.1:n.189+3577A>T

Variant summary

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

The ENST00000809739.1(ENSG00000305238):​n.189+3577A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,966 control chromosomes in the GnomAD database, including 9,589 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 0.30 (9589 hom., cov: 32)
• Consequence: ENSG00000305238 ENST00000809739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 2 publications found

Genes affected

ENSG00000305238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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
ENSG00000305238	ENST00000809739.1	n.189+3577A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46212 AN: 151848 Hom.: 9556 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.305 AC: 46317 AN: 151966 Hom.: 9589 Cov.: 32 AF XY: 0.303 AC XY: 22528 AN XY: 74286

African (AFR) AF: 0.591 AC: 24460 AN: 41418

American (AMR) AF: 0.271 AC: 4137 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.151 AC: 781 AN: 5170

South Asian (SAS) AF: 0.167 AC: 804 AN: 4816

European-Finnish (FIN) AF: 0.244 AC: 2574 AN: 10548

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12200 AN: 67968

Other (OTH) AF: 0.275 AC: 580 AN: 2106

Alfa AF: 0.252 Hom.: 871

Bravo AF: 0.319

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs8008858; hg19: chr14-55379215;