rs10520131

Positions:

• chr15-39486279-G-A

Variant summary

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

The ENST00000654986.1(ENSG00000259269):​n.911+5211G>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 0.083 in 152,222 control chromosomes in the GnomAD database, including 979 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 0.083 (979 hom., cov: 32)
• Consequence: ENST00000654986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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
	ENST00000654986.1	n.911+5211G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12606 AN: 152104 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0830 AC: 12628 AN: 152222 Hom.: 979 Cov.: 32 AF XY: 0.0795 AC XY: 5920 AN XY: 74444

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0353

Gnomad4 SAS AF: 0.0528

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0332

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0528 Hom.: 112

Bravo AF: 0.0919

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520131; hg19: chr15-39778480;