rs17136138

chr5-113963340-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007058906.1(LOC124901047):n.2086-34836A>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 0.0338 in 152,100 control chromosomes in the GnomAD database, including 110 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 0.034 (110 hom., cov: 32)
• Consequence: LOC124901047 XR_007058906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

LOC124901047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0338 (5134/152100) while in subpopulation AFR AF= 0.0494 (2052/41502). AF 95% confidence interval is 0.0477. There are 110 homozygotes in gnomad4. There are 2440 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901047	XR_007058906.1	n.2086-34836A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5129 AN: 151982 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0338 AC: 5134 AN: 152100 Hom.: 110 Cov.: 32 AF XY: 0.0328 AC XY: 2440 AN XY: 74358

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.0278

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0331 Hom.: 16

Bravo AF: 0.0362

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.8
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17136138; hg19: chr5-113299037;