rs756136890

Variant names:

• chr18-47028616-G-A
• rs756136890
• NM_001387690.1:c.52-17841G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-47028616-G-A
• chr18-47028616-G-T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NM_001387690.1(KATNAL2):​c.52-17841G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: not found (cov: 8)
  • Exomes 𝑓: 0.0000016 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KATNAL2 NM_001387690.1 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.0880
• Publications: 0 publications found

Genes affected

KATNAL2 (HGNC:25387): (katanin catalytic subunit A1 like 2) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Located in cytoplasm; microtubule; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

ELOA3P (HGNC:24617): (elongin A3, pseudogene) The SIII (or elongin) transcription elongation factor complex stimulates the rate of transcription elongation by RNA polymerase II by suppressing the transient pausing of the polymerase at many sites along the DNA template. This gene represents a likely pseudogene of ELOA (GeneID: 6924). [provided by RefSeq, Jun 2020]

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP6: Variant 18-47028616-G-A is Benign according to our data. Variant chr18-47028616-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 3349331.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387690.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL2	NM_001387690.1	MANE Select	c.52-17841G>A		intron	N/A	NP_001374619.1	Q8IYT4-1
	KATNAL2	NM_001353899.1		c.130-17841G>A		intron	N/A	NP_001340828.1
	KATNAL2	NM_001353900.1		c.130-17841G>A		intron	N/A	NP_001340829.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL2	ENST00000683218.1	MANE Select	c.52-17841G>A		intron	N/A	ENSP00000508137.1	Q8IYT4-1
	KATNAL2	ENST00000245121.10	TSL:1	c.-94-24264G>A		intron	N/A	ENSP00000245121.4	Q8IYT4-2
	KATNAL2	ENST00000591522.2	TSL:1	c.-1-29619G>A		intron	N/A	ENSP00000467488.2	K7EPQ6

Frequencies

GnomAD3 genomes Cov.: 8

GnomAD2 exomes AF: 0.000154 AC: 28 AN: 181810 AF XY: 0.000150

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00249

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000162 AC: 1 AN: 615878 Hom.: 0 Cov.: 6 AF XY: 0.00000322 AC XY: 1 AN XY: 310158

African (AFR) AF: 0.00 AC: 0 AN: 16330

American (AMR) AF: 0.00 AC: 0 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13948

East Asian (EAS) AF: 0.00 AC: 0 AN: 14756

South Asian (SAS) AF: 0.00 AC: 0 AN: 40482

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2296

European-Non Finnish (NFE) AF: 0.00000216 AC: 1 AN: 463408

Other (OTH) AF: 0.00 AC: 0 AN: 27900

GnomAD4 genome Cov.: 8

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	ELOA3P-related condition (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.0
DANN	Benign	0.83
PhyloP100		-0.088

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs756136890; hg19: chr18-44554987;