5-113963296-C-A

Variant names:

• chr5-113963296-C-A
• rs10519366
• XR_007058906.1:n.2086-34880C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058906.1(LOC124901047):​n.2086-34880C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,050 control chromosomes in the GnomAD database, including 3,529 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 0.21 (3529 hom., cov: 32)
• Consequence: LOC124901047 XR_007058906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901047	XR_007058906.1	n.2086-34880C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31380 AN: 151932 Hom.: 3529 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.206 AC: 31382 AN: 152050 Hom.: 3529 Cov.: 32 AF XY: 0.207 AC XY: 15409 AN XY: 74324

African (AFR) AF: 0.129 AC: 5373 AN: 41500

American (AMR) AF: 0.199 AC: 3039 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3470

East Asian (EAS) AF: 0.162 AC: 834 AN: 5154

South Asian (SAS) AF: 0.233 AC: 1122 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16562 AN: 67964

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.222 Hom.: 12020

Bravo AF: 0.196

Asia WGS AF: 0.226 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.48
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10519366; hg19: chr5-113298993; COSMIC: COSV60184259;