14-87039904-A-T

Variant names:

• chr14-87039904-A-T
• rs11624056
• ENST00000733865.1:n.238-6209T>A

Variant summary

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

The ENST00000733865.1(ENSG00000295909):​n.238-6209T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 152,062 control chromosomes in the GnomAD database, including 697 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 0.081 (697 hom., cov: 31)
• Consequence: ENSG00000295909 ENST00000733865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508
• Publications: 10 publications found

Genes affected

ENSG00000295909 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733865.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295909	ENST00000733865.1		n.238-6209T>A		intron	N/A
	ENSG00000295909	ENST00000733866.1		n.124-6209T>A		intron	N/A
	ENSG00000295909	ENST00000733867.1		n.96-6218T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12260 AN: 151944 Hom.: 698 Cov.: 31

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0806 AC: 12257 AN: 152062 Hom.: 697 Cov.: 31 AF XY: 0.0791 AC XY: 5881 AN XY: 74312

African (AFR) AF: 0.0237 AC: 983 AN: 41518

American (AMR) AF: 0.0562 AC: 858 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.0119 AC: 61 AN: 5134

South Asian (SAS) AF: 0.129 AC: 623 AN: 4818

European-Finnish (FIN) AF: 0.0961 AC: 1015 AN: 10558

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8285 AN: 67972

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0214 Hom.: 100

Bravo AF: 0.0724

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.60
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs11624056; hg19: chr14-87506248;