14-96631316-C-T

Variant names:

• chr14-96631316-C-T
• rs735408
• ENST00000846020.1:n.51+38501C>T

Variant summary

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

The ENST00000846020.1(ENSG00000258702):​n.51+38501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 151,982 control chromosomes in the GnomAD database, including 854 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 0.10 (854 hom., cov: 31)
• Consequence: ENSG00000258702 ENST00000846020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 4 publications found

Genes affected

ENSG00000258702 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846020.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258702	ENST00000846020.1		n.51+38501C>T		intron	N/A
	ENSG00000258702	ENST00000846021.1		n.51-36079C>T		intron	N/A
	ENSG00000258702	ENST00000846022.1		n.55-36079C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15408 AN: 151862 Hom.: 856 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.0682

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.101 AC: 15420 AN: 151982 Hom.: 854 Cov.: 31 AF XY: 0.101 AC XY: 7499 AN XY: 74282

African (AFR) AF: 0.128 AC: 5312 AN: 41424

American (AMR) AF: 0.0766 AC: 1170 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0682 AC: 236 AN: 3462

East Asian (EAS) AF: 0.108 AC: 556 AN: 5148

South Asian (SAS) AF: 0.188 AC: 904 AN: 4806

European-Finnish (FIN) AF: 0.0714 AC: 756 AN: 10586

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0917 AC: 6233 AN: 67964

Other (OTH) AF: 0.0940 AC: 198 AN: 2106

Alfa AF: 0.0881 Hom.: 889

Bravo AF: 0.100

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.47
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs735408; hg19: chr14-97097653;