NM_018179.5:c.-8+14729G>A

Variant names:

• chr12-14380556-G-A
• rs7312042
• NM_018179.5:c.-8+14729G>A

Variant summary

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

The NM_018179.5(ATF7IP):​c.-8+14729G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,084 control chromosomes in the GnomAD database, including 22,767 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 0.54 (22767 hom., cov: 32)
• Consequence: ATF7IP NM_018179.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 10 publications found

Genes affected

ATF7IP (HGNC:20092): (activating transcription factor 7 interacting protein) ATF7IP is a multifunctional nuclear protein that associates with heterochromatin. It can act as a transcriptional coactivator or corepressor depending upon its binding partners (summary by Liu et al., 2009 [PubMed 19106100]).[supplied by OMIM, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018179.5. 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
	ATF7IP	NM_018179.5	MANE Select	c.-8+14729G>A		intron	N/A	NP_060649.3
	ATF7IP	NM_001286514.2		c.-8+14729G>A		intron	N/A	NP_001273443.1	Q6VMQ6-5
	ATF7IP	NM_001286515.2		c.-8+14729G>A		intron	N/A	NP_001273444.1	Q6VMQ6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF7IP	ENST00000261168.9	TSL:5 MANE Select	c.-8+14729G>A		intron	N/A	ENSP00000261168.4	Q6VMQ6-1
	ATF7IP	ENST00000536444.5	TSL:1	c.-8+14729G>A		intron	N/A	ENSP00000445955.1	Q6VMQ6-5
	ATF7IP	ENST00000543189.5	TSL:1	c.-8+14729G>A		intron	N/A	ENSP00000443179.1	Q6VMQ6-2

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82312 AN: 151964 Hom.: 22722 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.542 AC: 82415 AN: 152084 Hom.: 22767 Cov.: 32 AF XY: 0.536 AC XY: 39822 AN XY: 74338

African (AFR) AF: 0.650 AC: 26984 AN: 41484

American (AMR) AF: 0.588 AC: 8981 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2058 AN: 5178

South Asian (SAS) AF: 0.495 AC: 2389 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4331 AN: 10556

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34412 AN: 67968

Other (OTH) AF: 0.527 AC: 1114 AN: 2112

Alfa AF: 0.512 Hom.: 10616

Bravo AF: 0.563

Asia WGS AF: 0.498 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.028
Mutation Taster		=100/0	polymorphism (auto)

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: rs7312042; hg19: chr12-14533490;