rs4147305

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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: ENST00000650784.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
C12orf42	XM_011538294.3	c.36+5425C>T		intron_variant			XP_011536596.1
C12orf42	XM_011538306.2	c.36+5425C>T		intron_variant			XP_011536608.1
C12orf42	XM_011538312.3	c.36+5425C>T		intron_variant			XP_011536614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650784.1	n.739C>T		non_coding_transcript_exon_variant	4/4

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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.0710

Gnomad4 OTH AF: 0.100

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4147305; hg19: chr12-103912465;