12-14500933-C-T

Variant summary

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

The NM_018179.5(ATF7IP):c.*2860C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,974 control chromosomes in the GnomAD database, including 7,404 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 0.28 (7404 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATF7IP NM_018179.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATF7IP	NM_018179.5	c.*2860C>T		3_prime_UTR_variant	15/15	ENST00000261168.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATF7IP	ENST00000261168.9	c.*2860C>T		3_prime_UTR_variant	15/15	5	NM_018179.5	P5
ATF7IP	ENST00000536444.5	c.*2860C>T		3_prime_UTR_variant	15/15	1		A2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42514 AN: 151856 Hom.: 7392 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.310

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.280 AC: 42540 AN: 151974 Hom.: 7404 Cov.: 32 AF XY: 0.280 AC XY: 20801 AN XY: 74224

Gnomad4 AFR AF: 0.0691

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.311

Alfa AF: 0.342 Hom.: 14858

Bravo AF: 0.288

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.3
Dann	Benign	0.42

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: rs2900333; hg19: chr12-14653867; COSMIC: COSV53691525; COSMIC: COSV53691525;