rs13335336

Positions:

• chr16-10465406-A-G
• chr16-10465406-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATF7IP2	NM_001393719.1	c.1353-6704A>G		intron_variant		ENST00000562102.6	NP_001380648.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATF7IP2	ENST00000562102.6	c.1353-6704A>G		intron_variant		4	NM_001393719.1	ENSP00000457731.2

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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0228

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0374 Hom.: 335

Bravo AF: 0.0861

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.52

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: rs13335336; hg19: chr16-10559263;