1-175160555-G-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014656.3(KIAA0040):​c.*159C>T 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_addAF=-0.374822).

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>T		3_prime_UTR	Exon 4 of 4	NP_055471.2
	KIAA0040	NM_001162893.2		c.*159C>T		3_prime_UTR	Exon 5 of 5	NP_001156365.1
	KIAA0040	NM_001162894.2		c.*159C>T		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>T		3_prime_UTR	Exon 4 of 4	ENSP00000462172.1
	KIAA0040	ENST00000444639.5	TSL:1	c.*159C>T		3_prime_UTR	Exon 4 of 4	ENSP00000463734.1
	KIAA0040	ENST00000545251.6	TSL:1	c.*159C>T		3_prime_UTR	Exon 3 of 3	ENSP00000464040.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 550398 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 284732

African (AFR) AF: 0.00 AC: 0 AN: 14206

American (AMR) AF: 0.00 AC: 0 AN: 17896

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14216

East Asian (EAS) AF: 0.00 AC: 0 AN: 31224

South Asian (SAS) AF: 0.00 AC: 0 AN: 45058

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30842

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2166

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 365522

Other (OTH) AF: 0.00 AC: 0 AN: 29268

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Uncertain	1.0
FATHMM_MKL	Benign	0.15	N
PhyloP100		1.5
Vest4		0.086
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;