rs1683151

Variant names:

• chr12-53552435-C-A
• rs1683151
• NM_006856.3:c.145+106G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-53552435-C-A
• chr12-53552435-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_006856.3(ATF7):​c.145+106G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000292 in 684,640 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: ATF7 NM_006856.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 0 publications found

Genes affected

ATF7 (HGNC:792): (activating transcription factor 7) Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; mitogen-activated protein kinase binding activity; and transcription coactivator binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. Biomarker of colorectal cancer. [provided by Alliance of Genome Resources, Apr 2022]

ATF7-NPFF (HGNC:55073): (ATF7-NPFF readthrough) Predicted to enable DNA binding activity and DNA-binding transcription factor activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285692 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006856.3. 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
	ATF7	NM_006856.3	MANE Select	c.145+106G>T		intron	N/A	NP_006847.1	P17544-6
	ATF7	NM_001366555.2		c.145+106G>T		intron	N/A	NP_001353484.1	P17544-1
	ATF7	NM_001366556.2		c.145+106G>T		intron	N/A	NP_001353485.1	P17544-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF7	ENST00000420353.7	TSL:1 MANE Select	c.145+106G>T		intron	N/A	ENSP00000399465.1	P17544-6
	ATF7-NPFF	ENST00000591834.1	TSL:5	c.145+106G>T		intron	N/A	ENSP00000466174.1	K7ELQ4
	ATF7	ENST00000548118.6	TSL:1	c.145+106G>T		intron	N/A	ENSP00000456858.1	P17544-5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000292 AC: 2 AN: 684640 Hom.: 0 AF XY: 0.00000279 AC XY: 1 AN XY: 358466

African (AFR) AF: 0.00 AC: 0 AN: 17482

American (AMR) AF: 0.00 AC: 0 AN: 29108

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18946

East Asian (EAS) AF: 0.00 AC: 0 AN: 33038

South Asian (SAS) AF: 0.0000325 AC: 2 AN: 61444

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47860

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3034

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 439558

Other (OTH) AF: 0.00 AC: 0 AN: 34170

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1683151; hg19: chr12-53946219;