rs10509488

Variant names:

• chr10-84016981-T-C
• rs10509488

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 0.0716 in 152,324 control chromosomes in the GnomAD database, including 513 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 0.072 (513 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 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: 0.0716 AC: 10896 AN: 152206 Hom.: 510 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0519

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0716 AC: 10914 AN: 152324 Hom.: 513 Cov.: 33 AF XY: 0.0699 AC XY: 5203 AN XY: 74488

African (AFR) AF: 0.122 AC: 5070 AN: 41554

American (AMR) AF: 0.0526 AC: 805 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.155 AC: 802 AN: 5186

South Asian (SAS) AF: 0.0513 AC: 248 AN: 4832

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10626

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3310 AN: 68030

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0660 Hom.: 66

Bravo AF: 0.0774

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.56
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10509488; hg19: chr10-85776737;