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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370030	XR_007063493.1	n.181A>C		non_coding_transcript_exon_variant	Exon 2 of 3
LOC105370030	XR_007063494.1	n.193A>C		non_coding_transcript_exon_variant	Exon 2 of 3
LOC105370030	XR_945453.3	n.193A>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302061	ENST00000783737.1	n.118A>C		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs3892756; hg19: chr12-121554668;