rs10842853

Variant names:

• chr12-27107481-T-C
• rs10842853

Your query was ambiguous. Multiple possible variants found:

• chr12-27107481-T-C
• chr12-27107481-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0916 in 152,270 control chromosomes in the GnomAD database, including 810 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 0.092 (810 hom., cov: 32)
• Consequence: LOC124902904 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 3 publications found

Genes affected

LOC124902904 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902904		n.27107481T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256226	ENST00000538920.1	n.244-2223A>G		intron_variant	Intron 1 of 1	5
ENSG00000256226	ENST00000824827.1	n.281-2223A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13957 AN: 152152 Hom.: 810 Cov.: 32

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0916 AC: 13955 AN: 152270 Hom.: 810 Cov.: 32 AF XY: 0.0906 AC XY: 6742 AN XY: 74450

African (AFR) AF: 0.0221 AC: 919 AN: 41566

American (AMR) AF: 0.0868 AC: 1328 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3470

East Asian (EAS) AF: 0.0287 AC: 149 AN: 5196

South Asian (SAS) AF: 0.0571 AC: 276 AN: 4832

European-Finnish (FIN) AF: 0.131 AC: 1382 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9089 AN: 68012

Other (OTH) AF: 0.0882 AC: 186 AN: 2110

Alfa AF: 0.0659 Hom.: 123

Bravo AF: 0.0863

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs10842853; hg19: chr12-27260414;