rs10520797

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000656202.1(ENSG00000275016):​n.47-5595G>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 ENST00000656202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38
• Publications: 3 publications found

Genes affected

ENSG00000275016 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656202.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275016	ENST00000611285.1	TSL:5	n.26+8734G>A		intron	N/A
	ENSG00000275016	ENST00000612595.2	TSL:5	n.204+8734G>A		intron	N/A
	ENSG00000275016	ENST00000614344.6	TSL:5	n.201+8734G>A		intron	N/A

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

African (AFR) AF: 0.322 AC: 13370 AN: 41522

American (AMR) AF: 0.0808 AC: 1235 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5172

South Asian (SAS) AF: 0.138 AC: 665 AN: 4818

European-Finnish (FIN) AF: 0.0859 AC: 912 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3500 AN: 68020

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.0713 Hom.: 461

Bravo AF: 0.146

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	21
DANN	Benign	0.76
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs10520797; hg19: chr15-96190482;