rs17242130

Positions:

• chr5-81859087-A-C

Variant summary

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

The XR_007058843.1(LOC124901018):​n.230+5057A>C 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 0.0795 in 151,512 control chromosomes in the GnomAD database, including 559 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 0.079 (559 hom., cov: 31)
• Consequence: LOC124901018 XR_007058843.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648

Genes affected

LOC124901018 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901018	XR_007058843.1	n.230+5057A>C		intron_variant, non_coding_transcript_variant
LOC124901018	XR_007058844.1	n.230+5057A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12036 AN: 151410 Hom.: 560 Cov.: 31

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0795 AC: 12042 AN: 151512 Hom.: 559 Cov.: 31 AF XY: 0.0765 AC XY: 5658 AN XY: 73988

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.000776

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0883

Alfa AF: 0.102 Hom.: 1129

Bravo AF: 0.0795

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17242130; hg19: chr5-81154906;