rs10520797

Variant names:

• chr15-95647253-G-A
• rs10520797
• ENST00000611285.1:n.26+8734G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000611285.1(ENSG00000275016):​n.26+8734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,224 control chromosomes in the GnomAD database, including 2,575 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 (2575 hom., cov: 34)
• Consequence: ENSG00000275016 ENST00000611285.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38

Genes affected

ENSG00000275016 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275016	ENST00000611285.1	n.26+8734G>A		intron_variant	Intron 1 of 1	5
ENSG00000275016	ENST00000612595.2	n.204+8734G>A		intron_variant	Intron 1 of 2	5
ENSG00000275016	ENST00000614344.5	n.193+8734G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21155 AN: 152106 Hom.: 2571 Cov.: 34

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.139 AC: 21181 AN: 152224 Hom.: 2575 Cov.: 34 AF XY: 0.141 AC XY: 10517 AN XY: 74430

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0723 Hom.: 425

Bravo AF: 0.146

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	21
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520797; hg19: chr15-96190482;