12-14480289-A-G

Variant names:

• chr12-14480289-A-G
• rs11055991
• NM_018179.5:c.3098-714A>G

Variant summary

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

The NM_018179.5(ATF7IP):​c.3098-714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,070 control chromosomes in the GnomAD database, including 9,066 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 0.31 (9066 hom., cov: 32)
• Consequence: ATF7IP NM_018179.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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.3098-714A>G		intron	N/A	NP_060649.3
	ATF7IP	NM_181352.2		c.3122-714A>G		intron	N/A	NP_851997.1	Q6VMQ6-4
	ATF7IP	NM_001388179.1		c.3119-714A>G		intron	N/A	NP_001375108.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF7IP	ENST00000261168.9	TSL:5 MANE Select	c.3098-714A>G		intron	N/A	ENSP00000261168.4	Q6VMQ6-1
	ATF7IP	ENST00000544627.5	TSL:1	c.3122-714A>G		intron	N/A	ENSP00000440440.1	Q6VMQ6-4
	ATF7IP	ENST00000540793.5	TSL:1	c.3098-714A>G		intron	N/A	ENSP00000444589.1	Q6VMQ6-1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47620 AN: 151950 Hom.: 9056 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.313 AC: 47641 AN: 152070 Hom.: 9066 Cov.: 32 AF XY: 0.313 AC XY: 23263 AN XY: 74326

African (AFR) AF: 0.0860 AC: 3571 AN: 41524

American (AMR) AF: 0.461 AC: 7038 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1777 AN: 5180

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4826

European-Finnish (FIN) AF: 0.316 AC: 3335 AN: 10570

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27480 AN: 67920

Other (OTH) AF: 0.352 AC: 741 AN: 2108

Alfa AF: 0.359 Hom.: 3484

Bravo AF: 0.320

Asia WGS AF: 0.407 AC: 1407 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-1.1
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: rs11055991; hg19: chr12-14633223; COSMIC: COSV53772250; COSMIC: COSV53772250;