rs10488475

Variant names:

• chr7-17773820-C-T
• rs10488475

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 0.0726 in 151,914 control chromosomes in the GnomAD database, including 505 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 0.073 (505 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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: 0.0726 AC: 11026 AN: 151798 Hom.: 506 Cov.: 29

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0439

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0726 AC: 11028 AN: 151914 Hom.: 505 Cov.: 29 AF XY: 0.0746 AC XY: 5542 AN XY: 74248

African (AFR) AF: 0.0312 AC: 1293 AN: 41420

American (AMR) AF: 0.0642 AC: 978 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0439 AC: 152 AN: 3466

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5162

South Asian (SAS) AF: 0.146 AC: 703 AN: 4804

European-Finnish (FIN) AF: 0.126 AC: 1330 AN: 10544

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6330 AN: 67956

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0839 Hom.: 1083

Bravo AF: 0.0656

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.48
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs10488475; hg19: chr7-17813444;