chr1-175160555-G-C

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 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
• Publications: 21 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014656.3. 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
	KIAA0040	NM_014656.3	MANE Select	c.*159C>G		3_prime_UTR	Exon 4 of 4	NP_055471.2
	KIAA0040	NM_001162893.2		c.*159C>G		3_prime_UTR	Exon 5 of 5	NP_001156365.1
	KIAA0040	NM_001162894.2		c.*159C>G		3_prime_UTR	Exon 4 of 4	NP_001156366.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0040	ENST00000423313.6	TSL:1 MANE Select	c.*159C>G		3_prime_UTR	Exon 4 of 4	ENSP00000462172.1
	KIAA0040	ENST00000444639.5	TSL:1	c.*159C>G		3_prime_UTR	Exon 4 of 4	ENSP00000463734.1
	KIAA0040	ENST00000545251.6	TSL:1	c.*159C>G		3_prime_UTR	Exon 3 of 3	ENSP00000464040.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 7

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.099
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
PhyloP100		1.5
Vest4		0.10
MVP		0.27
GERP RS		4.5
Mutation Taster		=100/0	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: rs2269650; hg19: chr1-175129691;