rs10520722

Positions:

• chr15-93362604-T-A

Variant summary

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

The ENST00000667030.1(ENSG00000257060):​n.236+103367T>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 0.392 in 151,982 control chromosomes in the GnomAD database, including 12,142 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 0.39 (12142 hom., cov: 32)
• Consequence: ENST00000667030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370982	XR_007064770.1	n.1161-10906T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667030.1	n.236+103367T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59542 AN: 151864 Hom.: 12131 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.392 AC: 59596 AN: 151982 Hom.: 12142 Cov.: 32 AF XY: 0.385 AC XY: 28591 AN XY: 74266

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.364

Alfa AF: 0.421 Hom.: 1684

Bravo AF: 0.390

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520722; hg19: chr15-93905833;