14-84131041-G-C

Variant names:

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

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>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 152,270 control chromosomes in the GnomAD database, including 472 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 0.073 (472 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0839 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

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
	ENSG00000285826	ENST00000649337.1		n.185+9319C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0730 AC: 11110 AN: 152152 Hom.: 473 Cov.: 33

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0730 AC: 11116 AN: 152270 Hom.: 472 Cov.: 33 AF XY: 0.0694 AC XY: 5166 AN XY: 74452

African (AFR) AF: 0.0857 AC: 3561 AN: 41542

American (AMR) AF: 0.0535 AC: 818 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5162

South Asian (SAS) AF: 0.0275 AC: 133 AN: 4832

European-Finnish (FIN) AF: 0.0322 AC: 342 AN: 10624

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0857 AC: 5830 AN: 68032

Other (OTH) AF: 0.0791 AC: 167 AN: 2110

Alfa AF: 0.00787 Hom.: 10278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.61
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7152554;

hg19: chr14-84597385;