rs8019707

Positions:

• chr14-55103122-T-G

Variant summary

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

The XR_007064177.1(LOC124903318):​n.200+8A>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 0.0626 in 152,244 control chromosomes in the GnomAD database, including 728 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 0.063 (728 hom., cov: 32)
• Consequence: LOC124903318 XR_007064177.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55103122T>G		intergenic_region
LOC124903318	XR_007064177.1	n.200+8A>C		splice_region_variant, intron_variant
LOC124903318	XR_007064178.1	n.189+19A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9520 AN: 152126 Hom.: 726 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00860

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0626 AC: 9536 AN: 152244 Hom.: 728 Cov.: 32 AF XY: 0.0615 AC XY: 4582 AN XY: 74448

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.00264

Gnomad4 NFE AF: 0.00858

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0277 Hom.: 49

Bravo AF: 0.0717

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8019707; hg19: chr14-55569840;