rs10508218

Variant names:

• chr10-1838286-G-C
• rs10508218

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 0.0926 in 152,292 control chromosomes in the GnomAD database, including 773 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 0.093 (773 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.134 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: 0.0925 AC: 14078 AN: 152174 Hom.: 771 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0926 AC: 14101 AN: 152292 Hom.: 773 Cov.: 33 AF XY: 0.0887 AC XY: 6604 AN XY: 74466

African (AFR) AF: 0.137 AC: 5699 AN: 41550

American (AMR) AF: 0.0719 AC: 1100 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.0200 AC: 104 AN: 5192

South Asian (SAS) AF: 0.101 AC: 486 AN: 4826

European-Finnish (FIN) AF: 0.0274 AC: 291 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0876 AC: 5958 AN: 68020

Other (OTH) AF: 0.0785 AC: 166 AN: 2114

Alfa AF: 0.0920 Hom.: 100

Bravo AF: 0.0980

Asia WGS AF: 0.0690 AC: 241 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	8.4
DANN	Benign	0.61
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10508218; hg19: chr10-1880480;