rs10849846

Variant names:

• chr12-121120620-T-C
• rs10849846

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 0.141 in 152,046 control chromosomes in the GnomAD database, including 2,711 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 0.14 (2711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.141 AC: 21356 AN: 151928 Hom.: 2704 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.141 AC: 21400 AN: 152046 Hom.: 2711 Cov.: 32 AF XY: 0.142 AC XY: 10545 AN XY: 74344

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.0585

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0598 Hom.: 557

Bravo AF: 0.146

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10849846; hg19: chr12-121558423;