rs4792734

Positions:

• chr17-8304837-A-G
• chr17-8304837-A-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_Moderate BA1

The XR_007065605.1(LOC124903914):​n.450-2A>G variant causes a splice acceptor, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,116 control chromosomes in the GnomAD database, including 4,413 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 0.20 (4413 hom., cov: 31)
• Consequence: LOC124903914 XR_007065605.1 splice_acceptor, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

Genes affected

LOC124903915 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903915	XR_007065606.1	n.14T>C		non_coding_transcript_exon_variant	1/2
LOC124903914	XR_007065605.1	n.450-2A>G		splice_acceptor_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29914 AN: 151998 Hom.: 4399 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.197 AC: 29957 AN: 152116 Hom.: 4413 Cov.: 31 AF XY: 0.203 AC XY: 15116 AN XY: 74366

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.0805

Gnomad4 OTH AF: 0.185

Alfa AF: 0.111 Hom.: 3358

Bravo AF: 0.216

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4792734; hg19: chr17-8208155;