rs8010717

Positions:

• chr14-79944098-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001751015.3(LOC107984630):​n.86+6T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,104 control chromosomes in the GnomAD database, including 6,229 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 0.29 (6229 hom., cov: 33)
• Consequence: LOC107984630 XR_001751015.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

ENSG00000258416 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984630	XR_001751015.3	n.86+6T>C		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258416	ENST00000554307.1	n.366+28204A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43357 AN: 151986 Hom.: 6216 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.285 AC: 43412 AN: 152104 Hom.: 6229 Cov.: 33 AF XY: 0.289 AC XY: 21470 AN XY: 74328

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.255

Alfa AF: 0.279 Hom.: 1101

Bravo AF: 0.279

Asia WGS AF: 0.271 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8010717; hg19: chr14-80410441;