rs10512468

Positions:

• chr17-35273933-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.243 in 152,064 control chromosomes in the GnomAD database, including 5,533 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 0.24 (5533 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36963 AN: 151946 Hom.: 5537 Cov.: 31

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.00500

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.243 AC: 36960 AN: 152064 Hom.: 5533 Cov.: 31 AF XY: 0.241 AC XY: 17901 AN XY: 74328

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.275

Alfa AF: 0.302 Hom.: 3712

Bravo AF: 0.229

Asia WGS AF: 0.0850 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512468; hg19: chr17-33600952;