rs10849846

Variant names:

• chr12-121120620-T-C
• rs10849846
• ENST00000783737.1:n.860T>C

Variant summary

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

The ENST00000783737.1(ENSG00000302061):​n.860T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302061 ENST00000783737.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 5 publications found

Genes affected

ENSG00000302061 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783737.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302061	ENST00000783737.1		n.860T>C		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.333 AC: 13810 AN: 41424

American (AMR) AF: 0.0585 AC: 893 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1384 AN: 5156

South Asian (SAS) AF: 0.136 AC: 655 AN: 4820

European-Finnish (FIN) AF: 0.0912 AC: 964 AN: 10574

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3309 AN: 68006

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.0696 Hom.: 985

Bravo AF: 0.146

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.23
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10849846; hg19: chr12-121558423;