rs6737169

chr2-38350559-T-C

Variant summary

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

The NM_001135673.4(ATL2):c.119-7047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,024 control chromosomes in the GnomAD database, including 6,579 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 0.29 (6579 hom., cov: 31)
• Consequence: ATL2 NM_001135673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

Genes affected

ATL2 (HGNC:24047): (atlastin GTPase 2) Enables identical protein binding activity. Involved in Golgi organization; endoplasmic reticulum tubular network membrane organization; and protein homooligomerization. Located in endoplasmic reticulum tubular network membrane. Is integral component of membrane. [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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATL2	NM_001135673.4	c.119-7047A>G		intron_variant		ENST00000378954.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATL2	ENST00000378954.9	c.119-7047A>G		intron_variant		1	NM_001135673.4	P1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44273 AN: 151904 Hom.: 6573 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.291 AC: 44315 AN: 152024 Hom.: 6579 Cov.: 31 AF XY: 0.293 AC XY: 21797 AN XY: 74304

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.266

Alfa AF: 0.302 Hom.: 876

Bravo AF: 0.284

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.13
Dann	Benign	0.41

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: rs6737169; hg19: chr2-38577701;