rs10515234

Positions:

• chr5-96000627-T-C

Variant summary

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

The NR_130776.1(LOC101929710):​n.36+38591T>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 0.069 in 152,206 control chromosomes in the GnomAD database, including 733 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 0.069 (733 hom., cov: 32)
• Consequence: LOC101929710 NR_130776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929710	NR_130776.1	n.36+38591T>C		intron_variant, non_coding_transcript_variant
LOC105379096	XR_001742447.2	n.165-12440A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000502645.2	n.36+38591T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000511775.1	n.35+38591T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0688 AC: 10468 AN: 152088 Hom.: 726 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0592

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

GnomAD4 genome AF: 0.0690 AC: 10498 AN: 152206 Hom.: 733 Cov.: 32 AF XY: 0.0701 AC XY: 5215 AN XY: 74432

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0902

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.0218

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0521 Hom.: 87

Bravo AF: 0.0780

Asia WGS AF: 0.0740 AC: 256 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	0.44
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515234; hg19: chr5-95336331;