rs6837335

chr4-48361966-A-G

Variant summary

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

The NM_020846.2(SLAIN2):c.390-7883A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,034 control chromosomes in the GnomAD database, including 26,253 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 0.58 (26253 hom., cov: 33)
• Consequence: SLAIN2 NM_020846.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854

Genes affected

SLAIN2 (HGNC:29282): (SLAIN motif family member 2) Involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Located in centrosome and cytosol. Colocalizes with microtubule plus-end. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLAIN2	NM_020846.2	c.390-7883A>G		intron_variant		ENST00000264313.11
SLAIN2	XM_005248121.4	c.390-7883A>G		intron_variant
SLAIN2	XM_047416023.1	c.-34-7883A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLAIN2	ENST00000264313.11	c.390-7883A>G		intron_variant		1	NM_020846.2	P1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88334 AN: 151916 Hom.: 26240 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.581 AC: 88383 AN: 152034 Hom.: 26253 Cov.: 33 AF XY: 0.577 AC XY: 42852 AN XY: 74312

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.581

Alfa AF: 0.598 Hom.: 4498

Bravo AF: 0.570

Asia WGS AF: 0.583 AC: 2024 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.25
Dann	Benign	0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs6837335; hg19: chr4-48363983;