rs762048546

Variant names:

• chr16-10430856-C-A
• NM_001393719.1:c.236C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-10430856-C-A
• chr16-10430856-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001393719.1(ATF7IP2):​c.236C>A​(p.Ser79Tyr) 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. 13/21 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: 32)
• Consequence: ATF7IP2 NM_001393719.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13671562).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATF7IP2	NM_001393719.1	c.236C>A	p.Ser79Tyr	missense_variant	Exon 5 of 14	ENST00000562102.6	NP_001380648.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATF7IP2	ENST00000562102.6	c.236C>A	p.Ser79Tyr	missense_variant	Exon 5 of 14	4	NM_001393719.1	ENSP00000457731.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.089	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.023	T;.;.;.;T
Eigen	Benign	0.093
Eigen_PC	Benign	-0.041
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.79	.;.;T;T;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.14	T;T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	1.9	L;L;.;L;L
PrimateAI	Benign	0.39	T
PROVEAN	Uncertain	-2.4	N;D;D;D;N
REVEL	Benign	0.14
Sift	Pathogenic	0.0	D;D;D;D;D
Sift4G	Uncertain	0.0020	D;D;D;D;D
Polyphen		1.0	D;D;.;D;D
Vest4		0.32
MutPred		0.15		Loss of methylation at K81 (P = 0.0633);Loss of methylation at K81 (P = 0.0633);Loss of methylation at K81 (P = 0.0633);Loss of methylation at K81 (P = 0.0633);Loss of methylation at K81 (P = 0.0633);
MVP		0.20
MPC		0.057
ClinPred		0.75	D
GERP RS		4.3
Varity_R		0.18
gMVP		0.12

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-10524713;