rs10518834

Variant names:

• chr15-56052868-A-G
• rs10518834

Variant summary

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

The variant allele was found at a frequency of 0.305 in 152,084 control chromosomes in the GnomAD database, including 7,427 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 0.30 (7427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46351 AN: 151966 Hom.: 7426 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.305 AC: 46380 AN: 152084 Hom.: 7427 Cov.: 32 AF XY: 0.302 AC XY: 22436 AN XY: 74344

African (AFR) AF: 0.240 AC: 9944 AN: 41502

American (AMR) AF: 0.280 AC: 4273 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3470

East Asian (EAS) AF: 0.0328 AC: 170 AN: 5180

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4808

European-Finnish (FIN) AF: 0.369 AC: 3889 AN: 10548

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24500 AN: 67982

Other (OTH) AF: 0.293 AC: 618 AN: 2110

Alfa AF: 0.338 Hom.: 37472

Bravo AF: 0.295

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.43
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10518834; hg19: chr15-56345066;