14-98309160-A-C

Variant names:

• chr14-98309160-A-C
• rs8015534
• ENST00000751340.1:n.147+10616A>C

Variant summary

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

The ENST00000751340.1(ENSG00000297837):​n.147+10616A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,250 control chromosomes in the GnomAD database, including 1,163 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 0.11 (1163 hom., cov: 33)
• Consequence: ENSG00000297837 ENST00000751340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 2 publications found

Genes affected

ENSG00000297837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297837	ENST00000751340.1	n.147+10616A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17206 AN: 152132 Hom.: 1163 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.113 AC: 17225 AN: 152250 Hom.: 1163 Cov.: 33 AF XY: 0.113 AC XY: 8445 AN XY: 74458

African (AFR) AF: 0.176 AC: 7302 AN: 41536

American (AMR) AF: 0.107 AC: 1630 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5186

South Asian (SAS) AF: 0.167 AC: 808 AN: 4832

European-Finnish (FIN) AF: 0.108 AC: 1147 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5610 AN: 68000

Other (OTH) AF: 0.107 AC: 227 AN: 2116

Alfa AF: 0.0965 Hom.: 427

Bravo AF: 0.115

Asia WGS AF: 0.101 AC: 350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.79
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs8015534; hg19: chr14-98775497;