rs10849023

Variant names:

• chr12-4223312-C-T
• rs10849023

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 0.219 in 152,170 control chromosomes in the GnomAD database, including 3,765 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 (3765 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.219 AC: 33304 AN: 152052 Hom.: 3759 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.219 AC: 33350 AN: 152170 Hom.: 3765 Cov.: 33 AF XY: 0.221 AC XY: 16420 AN XY: 74402

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.232

Alfa AF: 0.211 Hom.: 6212

Bravo AF: 0.221

Asia WGS AF: 0.193 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.70
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10849023; hg19: chr12-4332478;