chr17-14618784-C-T

Variant names:

• chr17-14618784-C-T
• rs8074248
• XR_001753052.2:n.691-453C>T

Variant summary

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

The XR_001753052.2(LOC107984996):​n.691-453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,052 control chromosomes in the GnomAD database, including 4,789 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 0.25 (4789 hom., cov: 32)
• Consequence: LOC107984996 XR_001753052.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 6 publications found

Genes affected

LOC107984996 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38063 AN: 151934 Hom.: 4774 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.251 AC: 38118 AN: 152052 Hom.: 4789 Cov.: 32 AF XY: 0.252 AC XY: 18715 AN XY: 74312

African (AFR) AF: 0.267 AC: 11067 AN: 41470

American (AMR) AF: 0.256 AC: 3914 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1622 AN: 5140

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4816

European-Finnish (FIN) AF: 0.229 AC: 2421 AN: 10576

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16131 AN: 68004

Other (OTH) AF: 0.253 AC: 534 AN: 2110

Alfa AF: 0.241 Hom.: 12589

Bravo AF: 0.254

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.049
DANN	Benign	0.52
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs8074248; hg19: chr17-14522101;