rs2072035

Variant names:

• chr1-175160810-C-G
• rs2072035
• NM_014656.3:c.204G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-175160810-C-G
• chr1-175160810-C-T

Variant summary

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

The NM_014656.3(KIAA0040):​c.204G>C​(p.Lys68Asn) 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. 10/14 in silico tools predict 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: 25)
• Consequence: KIAA0040 NM_014656.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 15 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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14210856).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0040	NM_014656.3	MANE Select	c.204G>C	p.Lys68Asn	missense	Exon 4 of 4	NP_055471.2	Q15053
	KIAA0040	NM_001162893.2		c.204G>C	p.Lys68Asn	missense	Exon 5 of 5	NP_001156365.1	Q15053
	KIAA0040	NM_001162894.2		c.204G>C	p.Lys68Asn	missense	Exon 4 of 4	NP_001156366.1	Q15053

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0040	ENST00000423313.6	TSL:1 MANE Select	c.204G>C	p.Lys68Asn	missense	Exon 4 of 4	ENSP00000462172.1	Q15053
	KIAA0040	ENST00000444639.5	TSL:1	c.204G>C	p.Lys68Asn	missense	Exon 4 of 4	ENSP00000463734.1	Q15053
	KIAA0040	ENST00000545251.6	TSL:1	c.204G>C	p.Lys68Asn	missense	Exon 3 of 3	ENSP00000464040.1	Q15053

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 25

Alfa AF: 0.00 Hom.: 1970

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	7.2
DANN	Benign	0.89
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.46	T
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.14	T
PhyloP100		0.51
PrimateAI	Benign	0.46	T
Sift4G	Uncertain	0.046	D
Vest4		0.22
MVP		0.061
GERP RS		3.0
Varity_R		0.094
gMVP		0.031
Mutation Taster		=86/14	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: rs2072035; hg19: chr1-175129946;