rs17136138

Variant names:

• chr5-113963340-A-C
• rs17136138
• XR_007058906.1:n.2086-34836A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007058906.1(LOC124901047):​n.2086-34836A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 0 publications found

Genes affected

LOC124901047 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 110 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901047	XR_007058906.1	n.2086-34836A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0494 AC: 2052 AN: 41502

American (AMR) AF: 0.0278 AC: 424 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3472

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5158

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4822

European-Finnish (FIN) AF: 0.0197 AC: 209 AN: 10588

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2089 AN: 67990

Other (OTH) AF: 0.0451 AC: 95 AN: 2108

Alfa AF: 0.0337 Hom.: 17

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs17136138; hg19: chr5-113299037;