rs1894709

Variant names:

• chr1-175163235-G-T
• rs1894709
• NM_014656.3:c.-133-2089C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014656.3(KIAA0040):​c.-133-2089C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,078 control chromosomes in the GnomAD database, including 12,927 homozygotes. 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: 𝑓 0.41 (12927 hom., cov: 33)
• Consequence: KIAA0040 NM_014656.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 8 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

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.-133-2089C>A		intron	N/A	NP_055471.2	Q15053
	KIAA0040	NM_001162893.2		c.-133-2089C>A		intron	N/A	NP_001156365.1	Q15053
	KIAA0040	NM_001162894.2		c.-133-2089C>A		intron	N/A	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.-133-2089C>A		intron	N/A	ENSP00000462172.1	Q15053
	KIAA0040	ENST00000444639.5	TSL:1	c.-133-2089C>A		intron	N/A	ENSP00000463734.1	Q15053
	KIAA0040	ENST00000545251.6	TSL:1	c.-133-2089C>A		intron	N/A	ENSP00000464040.1	Q15053

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61659 AN: 151960 Hom.: 12930 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.393

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 61680 AN: 152078 Hom.: 12927 Cov.: 33 AF XY: 0.402 AC XY: 29909 AN XY: 74370

African (AFR) AF: 0.393 AC: 16304 AN: 41466

American (AMR) AF: 0.342 AC: 5230 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3470

East Asian (EAS) AF: 0.131 AC: 678 AN: 5176

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4824

European-Finnish (FIN) AF: 0.469 AC: 4959 AN: 10576

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30903 AN: 67968

Other (OTH) AF: 0.394 AC: 828 AN: 2104

Alfa AF: 0.417 Hom.: 12059

Bravo AF: 0.390

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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: rs1894709; hg19: chr1-175132371;