16-10465406-A-G

Variant names:

• chr16-10465406-A-G
• rs13335336
• NM_001393719.1:c.1353-6704A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393719.1(ATF7IP2):​c.1353-6704A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 152,088 control chromosomes in the GnomAD database, including 1,020 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 0.081 (1020 hom., cov: 29)
• Consequence: ATF7IP2 NM_001393719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

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.1353-6704A>G		intron	N/A	NP_001380648.1	Q5U623-1
	ATF7IP2	NM_001352120.2		c.1353-6704A>G		intron	N/A	NP_001339049.1	Q5U623-1
	ATF7IP2	NM_024997.5		c.1353-6704A>G		intron	N/A	NP_079273.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF7IP2	ENST00000562102.6	TSL:4 MANE Select	c.1353-6704A>G		intron	N/A	ENSP00000457731.2	Q5U623-1
	ATF7IP2	ENST00000356427.2	TSL:1	c.1353-6704A>G		intron	N/A	ENSP00000348799.2	Q5U623-1
	ATF7IP2	ENST00000396560.6	TSL:1	c.1353-6704A>G		intron	N/A	ENSP00000379808.2	Q5U623-1

Frequencies

GnomAD3 genomes AF: 0.0803 AC: 12208 AN: 151970 Hom.: 1011 Cov.: 29

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0805 AC: 12249 AN: 152088 Hom.: 1020 Cov.: 29 AF XY: 0.0802 AC XY: 5960 AN XY: 74352

African (AFR) AF: 0.203 AC: 8420 AN: 41448

American (AMR) AF: 0.0409 AC: 624 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.138 AC: 716 AN: 5176

South Asian (SAS) AF: 0.0941 AC: 452 AN: 4802

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10586

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0228 AC: 1551 AN: 68012

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0448 Hom.: 1243

Bravo AF: 0.0861

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.52
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs13335336; hg19: chr16-10559263;