chr10-5569948-C-T

Variant names:

• chr10-5569948-C-T
• rs12098712

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 0.13 in 152,158 control chromosomes in the GnomAD database, including 1,378 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 0.13 (1378 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 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: 0.130 AC: 19723 AN: 152040 Hom.: 1376 Cov.: 33

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.130 AC: 19749 AN: 152158 Hom.: 1378 Cov.: 33 AF XY: 0.131 AC XY: 9723 AN XY: 74396

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.127

Alfa AF: 0.137 Hom.: 284

Bravo AF: 0.128

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12098712; hg19: chr10-5611911;