NM_015915.5:c.862+3006T>C

Variant names:

• chr14-50617517-T-C
• rs17122693
• NM_015915.5:c.862+3006T>C

Variant summary

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

The NM_015915.5(ATL1):​c.862+3006T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,126 control chromosomes in the GnomAD database, including 2,822 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 0.18 (2822 hom., cov: 32)
• Consequence: ATL1 NM_015915.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911

Genes affected

ATL1 (HGNC:11231): (atlastin GTPase 1) The protein encoded by this gene is a GTPase and a Golgi body transmembrane protein. The encoded protein can form a homotetramer and has been shown to interact with spastin and with mitogen-activated protein kinase kinase kinase kinase 4. This protein may be involved in axonal maintenance as evidenced by the fact that defects in this gene are a cause of spastic paraplegia type 3. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATL1	NM_015915.5	c.862+3006T>C		intron_variant	Intron 8 of 13	ENST00000358385.12	NP_056999.2
ATL1	NM_001127713.1	c.862+3006T>C		intron_variant	Intron 9 of 13		NP_001121185.1
ATL1	NM_181598.4	c.862+3006T>C		intron_variant	Intron 8 of 12		NP_853629.2
ATL1	XM_047431430.1	c.862+3006T>C		intron_variant	Intron 9 of 14		XP_047287386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATL1	ENST00000358385.12	c.862+3006T>C		intron_variant	Intron 8 of 13	1	NM_015915.5	ENSP00000351155.7

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26803 AN: 152008 Hom.: 2822 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.176 AC: 26824 AN: 152126 Hom.: 2822 Cov.: 32 AF XY: 0.173 AC XY: 12890 AN XY: 74388

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0776

Gnomad4 SAS AF: 0.0774

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.167

Alfa AF: 0.136 Hom.: 3585

Bravo AF: 0.181

Asia WGS AF: 0.0980 AC: 340 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.70

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: rs17122693; hg19: chr14-51084235;