rs3892756

Variant names:

• chr12-121116865-A-C
• rs3892756
• ENST00000783737.1:n.118A>C

Variant summary

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

The ENST00000783737.1(ENSG00000302061):​n.118A>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 0.0661 in 152,202 control chromosomes in the GnomAD database, including 470 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 0.066 (470 hom., cov: 32)
• Consequence: ENSG00000302061 ENST00000783737.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0915 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302061	ENST00000783737.1		n.118A>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10070 AN: 152084 Hom.: 470 Cov.: 32

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0661 AC: 10065 AN: 152202 Hom.: 470 Cov.: 32 AF XY: 0.0659 AC XY: 4906 AN XY: 74414

African (AFR) AF: 0.0160 AC: 666 AN: 41564

American (AMR) AF: 0.0669 AC: 1022 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1346 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0934 AC: 6349 AN: 67990

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0752 Hom.: 382

Bravo AF: 0.0621

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.80
PhyloP100		0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3892756;

hg19: chr12-121554668;