NM_014656.3:c.*159C>G

Variant names:

• chr1-175160555-G-C
• rs2269650
• NM_014656.3:c.*159C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_014656.3(KIAA0040):​c.*159C>G variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KIAA0040 NM_014656.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

KIAA0040 (HGNC:28950): (KIAA0040) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.39254057).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.*159C>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313	c.*159C>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_014656.3	ENSP00000462172.1
KIAA0040	ENST00000444639	c.*159C>G		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000463734.1
KIAA0040	ENST00000545251	c.*159C>G		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000464040.1
KIAA0040	ENST00000619513.1	c.76C>G	p.Gln26Glu	missense_variant	Exon 2 of 2	2		ENSP00000478803.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 7

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.7
DANN	Benign	0.60
FATHMM_MKL	Benign	0.31	N
MetaRNN	Benign	0.39	T
Vest4		0.10
MVP		0.27
GERP RS		4.5

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: rs2269650; hg19: chr1-175129691;