rs9932051

Variant names:

• chr16-10480939-C-G
• rs9932051
• NM_001393719.1:c.1610C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-10480939-C-G
• chr16-10480939-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001393719.1(ATF7IP2):​c.1610C>G​(p.Thr537Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: ATF7IP2 NM_001393719.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944
• Publications: 8 publications found

Genes affected

ATF7IP2 (HGNC:20397): (activating transcription factor 7 interacting protein 2) Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.042140007).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393719.1. 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
	ATF7IP2	NM_001393719.1	MANE Select	c.1610C>G	p.Thr537Ser	missense	Exon 13 of 14	NP_001380648.1	Q5U623-1
	ATF7IP2	NM_001352120.2		c.1610C>G	p.Thr537Ser	missense	Exon 12 of 13	NP_001339049.1	Q5U623-1
	ATF7IP2	NM_024997.5		c.1610C>G	p.Thr537Ser	missense	Exon 11 of 12	NP_079273.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF7IP2	ENST00000562102.6	TSL:4 MANE Select	c.1610C>G	p.Thr537Ser	missense	Exon 13 of 14	ENSP00000457731.2	Q5U623-1
	ATF7IP2	ENST00000356427.2	TSL:1	c.1610C>G	p.Thr537Ser	missense	Exon 9 of 10	ENSP00000348799.2	Q5U623-1
	ATF7IP2	ENST00000396560.6	TSL:1	c.1610C>G	p.Thr537Ser	missense	Exon 11 of 12	ENSP00000379808.2	Q5U623-1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 928

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.093
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.063
DANN	Benign	0.32
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.013	N
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.0039	T
MetaRNN	Benign	0.042	T
MetaSVM	Benign	-0.94	T
PhyloP100		-0.94
PROVEAN	Benign	0.090	N
REVEL	Benign	0.10
Sift	Pathogenic	0.0	D
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.28
MutPred		0.14		Loss of glycosylation at P515 (P = 0.0274)
MVP		0.043
ClinPred		0.039	T
GERP RS		-6.5
Varity_R		0.031

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: rs9932051; hg19: chr16-10574796;