rs4147305

Variant names:

• chr12-103518687-G-A
• rs4147305
• ENST00000650784.1:n.739C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-103518687-G-A
• chr12-103518687-G-C

Variant summary

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

The ENST00000650784.1(ENSG00000286197):​n.739C>T 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 0.0966 in 152,042 control chromosomes in the GnomAD database, including 918 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 0.097 (918 hom., cov: 32)
• Consequence: ENSG00000286197 ENST00000650784.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 1 publications found

Genes affected

ENSG00000286197 (HGNC:):

C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf42	XM_047428802.1	c.36+5425C>T		intron_variant	Intron 2 of 6		XP_047284758.1
C12orf42	XM_047428803.1	c.-21-40240C>T		intron_variant	Intron 1 of 5		XP_047284759.1
C12orf42	XM_011538294.3	c.36+5425C>T		intron_variant	Intron 2 of 5		XP_011536596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286197	ENST00000650784.1	n.739C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0965 AC: 14660 AN: 151924 Hom.: 916 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.0966 AC: 14680 AN: 152042 Hom.: 918 Cov.: 32 AF XY: 0.0990 AC XY: 7357 AN XY: 74308

African (AFR) AF: 0.120 AC: 4975 AN: 41466

American (AMR) AF: 0.0678 AC: 1035 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1342 AN: 5160

South Asian (SAS) AF: 0.267 AC: 1280 AN: 4794

European-Finnish (FIN) AF: 0.0495 AC: 524 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4827 AN: 67974

Other (OTH) AF: 0.100 AC: 211 AN: 2106

Alfa AF: 0.0814 Hom.: 62

Bravo AF: 0.0960

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.81
DANN	Benign	0.67
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4147305; hg19: chr12-103912465;