chr17-56786087-G-A

Variant names:

• chr17-56786087-G-A
• rs10515134

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 0.0641 in 152,186 control chromosomes in the GnomAD database, including 375 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 0.064 (375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 13 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.112 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: 0.0641 AC: 9751 AN: 152068 Hom.: 373 Cov.: 32

Gnomad AFR AF: 0.0200

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.0976

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0641 AC: 9761 AN: 152186 Hom.: 375 Cov.: 32 AF XY: 0.0657 AC XY: 4886 AN XY: 74392

African (AFR) AF: 0.0201 AC: 834 AN: 41544

American (AMR) AF: 0.117 AC: 1781 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3470

East Asian (EAS) AF: 0.0976 AC: 505 AN: 5172

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4830

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10584

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4965 AN: 67986

Other (OTH) AF: 0.0630 AC: 133 AN: 2110

Alfa AF: 0.0680 Hom.: 963

Bravo AF: 0.0656

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10515134; hg19: chr17-54863448;