rs2861158

Positions:

• chr1-175166693-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000423313.6(KIAA0040):​c.-265C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,038 control chromosomes in the GnomAD database, including 4,929 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 0.22 (4929 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: KIAA0040 ENST00000423313.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.-265C>T		5_prime_UTR_variant	3/4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313.6	c.-265C>T		5_prime_UTR_variant	3/4	1	NM_014656.3	ENSP00000462172	P1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34042 AN: 151884 Hom.: 4921 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.167 AC: 6 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 4 AN XY: 24

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.200

GnomAD4 genome AF: 0.224 AC: 34054 AN: 152002 Hom.: 4929 Cov.: 32 AF XY: 0.226 AC XY: 16773 AN XY: 74282

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.269

Alfa AF: 0.282 Hom.: 10853

Bravo AF: 0.236

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.22		Position offset: 44

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2861158; hg19: chr1-175135829;