rs7312042

chr12-14380556-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATF7IP	NM_018179.5	c.-8+14729G>A		intron_variant		ENST00000261168.9
ATF7IP	NM_001286514.2	c.-8+14729G>A		intron_variant
ATF7IP	NM_001286515.2	c.-8+14729G>A		intron_variant
ATF7IP	NR_170893.1	n.146+14729G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATF7IP	ENST00000261168.9	c.-8+14729G>A		intron_variant		5	NM_018179.5	P5

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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.527

Alfa AF: 0.512 Hom.: 9588

Bravo AF: 0.563

Asia WGS AF: 0.498 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.9
Dann	Benign	0.65

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: rs7312042; hg19: chr12-14533490;