rs11055989

Positions:

• chr12-14469068-A-G
• chr12-14469068-A-T

Variant summary

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

The NM_018179.5(ATF7IP):​c.2862+2478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,032 control chromosomes in the GnomAD database, including 6,104 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 0.26 (6104 hom., cov: 31)
• Consequence: ATF7IP NM_018179.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.812

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATF7IP	NM_018179.5	c.2862+2478A>G		intron_variant		ENST00000261168.9	NP_060649.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATF7IP	ENST00000261168.9	c.2862+2478A>G		intron_variant		5	NM_018179.5	ENSP00000261168	P5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39280 AN: 151914 Hom.: 6102 Cov.: 31

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.258 AC: 39285 AN: 152032 Hom.: 6104 Cov.: 31 AF XY: 0.262 AC XY: 19482 AN XY: 74294

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.258

Alfa AF: 0.310 Hom.: 15804

Bravo AF: 0.232

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.3
DANN	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11055989; hg19: chr12-14622002;