rs10512468

Variant names:

• chr17-35273933-G-A
• rs10512468

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 0.243 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0961 AC: 3989 AN: 41494

American (AMR) AF: 0.238 AC: 3636 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3470

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5184

South Asian (SAS) AF: 0.193 AC: 930 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3466 AN: 10538

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22729 AN: 67968

Other (OTH) AF: 0.275 AC: 579 AN: 2102

Alfa AF: 0.303 Hom.: 4173

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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10512468; hg19: chr17-33600952;