rs12243558

Variant names:

• chr10-113180743-A-G
• rs12243558

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 0.337 in 152,262 control chromosomes in the GnomAD database, including 10,945 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 0.34 (10945 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.337 AC: 51296 AN: 152144 Hom.: 10913 Cov.: 34

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.337 AC: 51372 AN: 152262 Hom.: 10945 Cov.: 34 AF XY: 0.335 AC XY: 24975 AN XY: 74464

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.316

Alfa AF: 0.228 Hom.: 5924

Bravo AF: 0.357

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12243558; hg19: chr10-114940502;