rs12218935

Variant names:

• chr10-117989592-T-C
• rs12218935

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 0.455 in 152,142 control chromosomes in the GnomAD database, including 18,553 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 0.46 (18553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (NFE) allele frequency at 95% confidence interval = 0.596 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: 0.456 AC: 69268 AN: 152022 Hom.: 18546 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.455 AC: 69291 AN: 152142 Hom.: 18553 Cov.: 32 AF XY: 0.455 AC XY: 33845 AN XY: 74362

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.489

Alfa AF: 0.566 Hom.: 23488

Bravo AF: 0.423

Asia WGS AF: 0.380 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.21
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12218935; hg19: chr10-119749103;