rs10885392

Variant names:

• chr10-112933374-G-A
• rs10885392

Your query was ambiguous. Multiple possible variants found:

• chr10-112933374-G-A
• chr10-112933374-G-C
• chr10-112933374-G-T

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 0.218 in 151,796 control chromosomes in the GnomAD database, including 4,028 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 0.22 (4028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.271 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: 0.218 AC: 33043 AN: 151678 Hom.: 4023 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.218 AC: 33058 AN: 151796 Hom.: 4028 Cov.: 32 AF XY: 0.217 AC XY: 16089 AN XY: 74162

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0637

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.224

Alfa AF: 0.212 Hom.: 924

Bravo AF: 0.211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885392; hg19: chr10-114693133;