rs10035888

Positions:

• chr5-36348846-G-A

Variant summary

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

The XR_007058732.1(LOC124900962):​n.9013-1886G>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 0.399 in 151,778 control chromosomes in the GnomAD database, including 12,846 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 0.40 (12846 hom., cov: 30)
• Consequence: LOC124900962 XR_007058732.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

LOC124900962 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900962	XR_007058732.1	n.9013-1886G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60515 AN: 151660 Hom.: 12848 Cov.: 30

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.399 AC: 60528 AN: 151778 Hom.: 12846 Cov.: 30 AF XY: 0.395 AC XY: 29284 AN XY: 74164

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.402

Alfa AF: 0.444 Hom.: 1895

Bravo AF: 0.384

Asia WGS AF: 0.180 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10035888; hg19: chr5-36348948;