rs10505382

chr8-120916129-T-G

Variant summary

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

The ENST00000517739.1(ENSG00000253619):n.95+2970T>G 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 0.135 in 152,210 control chromosomes in the GnomAD database, including 1,425 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 0.14 (1425 hom., cov: 32)
• Consequence: ENST00000517739.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000517739.1	n.95+2970T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20566 AN: 152092 Hom.: 1421 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.135 AC: 20578 AN: 152210 Hom.: 1425 Cov.: 32 AF XY: 0.135 AC XY: 10077 AN XY: 74416

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.125

Alfa AF: 0.135 Hom.: 2843

Bravo AF: 0.133

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	3.5
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505382; hg19: chr8-121928369;