rs17157052

Variant names:

• chr10-1821357-A-G
• rs17157052

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 0.227 in 152,094 control chromosomes in the GnomAD database, including 4,153 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 0.23 (4153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 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: 0.227 AC: 34495 AN: 151976 Hom.: 4141 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.227 AC: 34557 AN: 152094 Hom.: 4153 Cov.: 32 AF XY: 0.227 AC XY: 16883 AN XY: 74360

African (AFR) AF: 0.253 AC: 10501 AN: 41476

American (AMR) AF: 0.234 AC: 3586 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1767 AN: 5140

South Asian (SAS) AF: 0.302 AC: 1451 AN: 4812

European-Finnish (FIN) AF: 0.187 AC: 1981 AN: 10600

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14017 AN: 67986

Other (OTH) AF: 0.213 AC: 448 AN: 2108

Alfa AF: 0.217 Hom.: 3397

Bravo AF: 0.231

Asia WGS AF: 0.332 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.094
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17157052; hg19: chr10-1863551;