chr14-84131041-G-A

Variant names:

• chr14-84131041-G-A
• rs7152554
• ENST00000649337.1:n.185+9319C>T

Variant summary

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

The ENST00000649337.1(ENSG00000285826):​n.185+9319C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,268 control chromosomes in the GnomAD database, including 52,905 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 0.83 (52905 hom., cov: 33)
• Consequence: ENSG00000285826 ENST00000649337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 4 publications found

Genes affected

ENSG00000285826 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649337.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285826	ENST00000649337.1		n.185+9319C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.828 AC: 126049 AN: 152150 Hom.: 52908 Cov.: 33

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.828 AC: 126087 AN: 152268 Hom.: 52905 Cov.: 33 AF XY: 0.829 AC XY: 61753 AN XY: 74454

African (AFR) AF: 0.701 AC: 29101 AN: 41542

American (AMR) AF: 0.816 AC: 12481 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3470

East Asian (EAS) AF: 0.668 AC: 3446 AN: 5160

South Asian (SAS) AF: 0.916 AC: 4424 AN: 4832

European-Finnish (FIN) AF: 0.934 AC: 9926 AN: 10622

Middle Eastern (MID) AF: 0.908 AC: 265 AN: 292

European-Non Finnish (NFE) AF: 0.893 AC: 60757 AN: 68034

Other (OTH) AF: 0.826 AC: 1744 AN: 2112

Alfa AF: 0.849 Hom.: 10278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.74
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7152554; hg19: chr14-84597385;