rs1485395

Positions:

• chr12-53601293-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006856.3(ATF7):​c.-21-272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,220 control chromosomes in the GnomAD database, including 2,133 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 0.16 (2133 hom., cov: 32)
• Consequence: ATF7 NM_006856.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATF7	NM_006856.3	c.-21-272A>G		intron_variant		ENST00000420353.7	NP_006847.1
ATF7-NPFF	NR_159377.1	n.105-272A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATF7	ENST00000420353.7	c.-21-272A>G		intron_variant		1	NM_006856.3	ENSP00000399465	P1
	ENST00000648881.1	n.475-6146T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25057 AN: 152098 Hom.: 2132 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.165 AC: 25065 AN: 152220 Hom.: 2133 Cov.: 32 AF XY: 0.161 AC XY: 12012 AN XY: 74442

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.156

Alfa AF: 0.170 Hom.: 4545

Bravo AF: 0.169

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs1485395; hg19: chr12-53995077;