rs7159947

Variant names:

• chr14-20341332-T-C
• rs7159947
• ENST00000749989.1:n.160-662A>G

Variant summary

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

The ENST00000749989.1(ENSG00000297673):​n.160-662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,936 control chromosomes in the GnomAD database, including 17,624 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 0.46 (17624 hom., cov: 32)
• Consequence: ENSG00000297673 ENST00000749989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 12 publications found

Genes affected

ENSG00000297673 (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 = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749989.1. 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
	ENSG00000297673	ENST00000749989.1		n.160-662A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69088 AN: 151818 Hom.: 17588 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.455 AC: 69184 AN: 151936 Hom.: 17624 Cov.: 32 AF XY: 0.451 AC XY: 33504 AN XY: 74256

African (AFR) AF: 0.703 AC: 29121 AN: 41438

American (AMR) AF: 0.344 AC: 5251 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1748 AN: 5172

South Asian (SAS) AF: 0.519 AC: 2500 AN: 4816

European-Finnish (FIN) AF: 0.361 AC: 3801 AN: 10530

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24345 AN: 67952

Other (OTH) AF: 0.426 AC: 896 AN: 2104

Alfa AF: 0.393 Hom.: 31728

Bravo AF: 0.462

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		-2.7

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: rs7159947;

hg19: chr14-20809491;