chr14-94628060-C-T

Variant names:

• chr14-94628060-C-T
• rs8005845
• ENST00000812399.1:n.184-8296G>A

Variant summary

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

The ENST00000812399.1(ENSG00000305687):​n.184-8296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,822 control chromosomes in the GnomAD database, including 37,335 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 0.70 (37335 hom., cov: 29)
• Consequence: ENSG00000305687 ENST00000812399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 10 publications found

Genes affected

ENSG00000305687 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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
ENSG00000305687	ENST00000812399.1	n.184-8296G>A		intron_variant	Intron 1 of 3
ENSG00000305687	ENST00000812400.1	n.322-8296G>A		intron_variant	Intron 1 of 2
ENSG00000305687	ENST00000812401.1	n.488-8296G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105942 AN: 151704 Hom.: 37311 Cov.: 29

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.698 AC: 106018 AN: 151822 Hom.: 37335 Cov.: 29 AF XY: 0.696 AC XY: 51618 AN XY: 74190

African (AFR) AF: 0.665 AC: 27496 AN: 41372

American (AMR) AF: 0.588 AC: 8982 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2639 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4586 AN: 5140

South Asian (SAS) AF: 0.708 AC: 3396 AN: 4794

European-Finnish (FIN) AF: 0.721 AC: 7607 AN: 10550

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48976 AN: 67918

Other (OTH) AF: 0.697 AC: 1469 AN: 2108

Alfa AF: 0.716 Hom.: 117092

Bravo AF: 0.690

Asia WGS AF: 0.807 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs8005845; hg19: chr14-95094397;