rs1392363801

Variant names:

• chr11-33542923-C-G
• rs1392363801
• NM_012194.3:c.1360C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-33542923-C-G
• chr11-33542923-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_012194.3(KIAA1549L):​c.1360C>G​(p.Pro454Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P454S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KIAA1549L NM_012194.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 0 publications found

Genes affected

KIAA1549L (HGNC:24836): (KIAA1549 like) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16471109).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012194.3. 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
	KIAA1549L	NM_012194.3	MANE Select	c.1360C>G	p.Pro454Ala	missense	Exon 2 of 21	NP_036326.3	A0A590UJI0
	KIAA1549L	NM_001410965.1		c.583+777C>G		intron	N/A	NP_001397894.1	H0YDE5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1549L	ENST00000658780.2	MANE Select	c.1360C>G	p.Pro454Ala	missense	Exon 2 of 21	ENSP00000499430.1	A0A590UJI0
	KIAA1549L	ENST00000265654.6	TSL:2	c.592C>G	p.Pro198Ala	missense	Exon 1 of 11	ENSP00000265654.6	A0A5F9UK30
	KIAA1549L	ENST00000526400.7	TSL:5	c.583+777C>G		intron	N/A	ENSP00000433481.3	H0YDE5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	21
DANN	Uncertain	0.98
DEOGEN2	Benign	0.036	T
Eigen	Benign	0.081
Eigen_PC	Benign	0.18
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.72	T
M_CAP	Benign	0.0055	T
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.0	L
PhyloP100		1.5
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.39	N
REVEL	Benign	0.14
Sift	Benign	0.048	D
Sift4G	Benign	0.52	T
Polyphen		0.97	D
Vest4		0.20
MutPred		0.34		Loss of loop (P = 0.0031)
MVP		0.37
MPC		0.31
ClinPred		0.25	T
GERP RS		3.3
Varity_R		0.025
gMVP		0.13
Mutation Taster		=92/8	polymorphism

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: rs1392363801; hg19: chr11-33564469;