14-94546047-A-G

Variant names:

• chr14-94546047-A-G
• rs11160190
• ENST00000658195.1:n.149-211A>G

Variant summary

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

The ENST00000658195.1(ENSG00000287668):​n.149-211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,168 control chromosomes in the GnomAD database, including 29,553 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 0.62 (29553 hom., cov: 34)
• Consequence: ENSG00000287668 ENST00000658195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 10 publications found

Genes affected

ENSG00000287668 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658195.1. 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
	ENSG00000287668	ENST00000658195.1		n.149-211A>G		intron	N/A
	ENSG00000294537	ENST00000724259.1		n.481-12407T>C		intron	N/A
	ENSG00000287668	ENST00000724367.1		n.460-211A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94060 AN: 152050 Hom.: 29530 Cov.: 34

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.619 AC: 94131 AN: 152168 Hom.: 29553 Cov.: 34 AF XY: 0.621 AC XY: 46234 AN XY: 74398

African (AFR) AF: 0.698 AC: 28957 AN: 41506

American (AMR) AF: 0.519 AC: 7930 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1814 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4188 AN: 5186

South Asian (SAS) AF: 0.680 AC: 3286 AN: 4830

European-Finnish (FIN) AF: 0.608 AC: 6435 AN: 10590

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39438 AN: 67974

Other (OTH) AF: 0.613 AC: 1297 AN: 2116

Alfa AF: 0.584 Hom.: 67652

Bravo AF: 0.613

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11160190; hg19: chr14-95012384;