chr4-48361966-A-G

Variant names:

• chr4-48361966-A-G
• rs6837335
• NM_020846.2:c.390-7883A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020846.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAIN2	NM_020846.2	MANE Select	c.390-7883A>G		intron	N/A	NP_065897.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAIN2	ENST00000264313.11	TSL:1 MANE Select	c.390-7883A>G		intron	N/A	ENSP00000264313.5

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

African (AFR) AF: 0.469 AC: 19424 AN: 41456

American (AMR) AF: 0.549 AC: 8385 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2383 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2562 AN: 5176

South Asian (SAS) AF: 0.708 AC: 3410 AN: 4818

European-Finnish (FIN) AF: 0.564 AC: 5939 AN: 10536

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.650 AC: 44158 AN: 67984

Other (OTH) AF: 0.581 AC: 1228 AN: 2114

Alfa AF: 0.612 Hom.: 42974

Bravo AF: 0.570

Asia WGS AF: 0.583 AC: 2024 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.55
PhyloP100		-0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs6837335; hg19: chr4-48363983;