rs10849023

Positions:

• chr12-4223312-C-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 0.219 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;