rs17466684

chr8-27595330-G-A

Variant summary

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

The XR_007060868.1(LOC124901919):n.1398-1737G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,068 control chromosomes in the GnomAD database, including 2,074 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 0.15 (2074 hom., cov: 32)
• Consequence: LOC124901919 XR_007060868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

LOC124901919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901919	XR_007060868.1	n.1398-1737G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22799 AN: 151950 Hom.: 2064 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.150 AC: 22824 AN: 152068 Hom.: 2074 Cov.: 32 AF XY: 0.154 AC XY: 11450 AN XY: 74304

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.138

Alfa AF: 0.168 Hom.: 3019

Bravo AF: 0.143

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	1.1
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17466684; hg19: chr8-27452847;