rs10520772

Variant names:

• chr15-95148210-A-G
• rs10520772
• ENST00000616940.1:n.235-4500A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658436.1(ENSG00000258773):​n.186+22T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 152,178 control chromosomes in the GnomAD database, including 87 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 0.029 (87 hom., cov: 32)
• Consequence: ENSG00000258773 ENST00000658436.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 0 publications found

Genes affected

ENSG00000293024 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658436.1. 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
	ENSG00000293024	ENST00000616940.1	TSL:5	n.235-4500A>G		intron	N/A
	ENSG00000258773	ENST00000658436.1		n.186+22T>C		intron	N/A
	ENSG00000258773	ENST00000658592.1		n.186+22T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4365 AN: 152062 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0117

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0287 AC: 4366 AN: 152178 Hom.: 87 Cov.: 32 AF XY: 0.0279 AC XY: 2075 AN XY: 74410

African (AFR) AF: 0.0528 AC: 2190 AN: 41484

American (AMR) AF: 0.0209 AC: 319 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5168

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4826

European-Finnish (FIN) AF: 0.0117 AC: 124 AN: 10606

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0205 AC: 1397 AN: 68018

Other (OTH) AF: 0.0317 AC: 67 AN: 2116

Alfa AF: 0.0276 Hom.: 31

Bravo AF: 0.0309

Asia WGS AF: 0.0110 AC: 40 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10520772;

hg19: chr15-95691439;