15-95148210-A-G

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 ENST00000616940.1(ENSG00000293024):​n.235-4500A>G 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: ENSG00000293024 ENST00000616940.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370991	XR_002957693.2	n.829-4500A>G		intron_variant	Intron 7 of 11
LOC105370990	XR_932646.3	n.235+22T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293024	ENST00000616940.1	n.235-4500A>G		intron_variant	Intron 3 of 5	5
ENSG00000258773	ENST00000658436.1	n.186+22T>C		intron_variant	Intron 2 of 3
ENSG00000258773	ENST00000658592.1	n.186+22T>C		intron_variant	Intron 2 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs10520772; hg19: chr15-95691439;