1-175160555-G-T

Position:

• chr1-175160555-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014656.3(KIAA0040):​c.*159C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 701,348 control chromosomes in the GnomAD database, including 54,272 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 0.38 (11463 hom., cov: 32)
  • Exomes 𝑓: 0.39 (42809 hom.)
• Consequence: KIAA0040 NM_014656.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0017420352).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.*159C>A		3_prime_UTR_variant	4/4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313	c.*159C>A		3_prime_UTR_variant	4/4	1	NM_014656.3	ENSP00000462172.1
KIAA0040	ENST00000444639	c.*159C>A		3_prime_UTR_variant	4/4	1		ENSP00000463734.1
KIAA0040	ENST00000545251	c.*159C>A		3_prime_UTR_variant	3/3	1		ENSP00000464040.1
KIAA0040	ENST00000619513.1	c.76C>A	p.Gln26Lys	missense_variant	2/2	2		ENSP00000478803.1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58063 AN: 151898 Hom.: 11442 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.388 AC: 213163 AN: 549332 Hom.: 42809 Cov.: 7 AF XY: 0.391 AC XY: 111011 AN XY: 284202

Gnomad4 AFR exome AF: 0.328

Gnomad4 AMR exome AF: 0.571

Gnomad4 ASJ exome AF: 0.522

Gnomad4 EAS exome AF: 0.544

Gnomad4 SAS exome AF: 0.428

Gnomad4 FIN exome AF: 0.370

Gnomad4 NFE exome AF: 0.358

Gnomad4 OTH exome AF: 0.396

GnomAD4 genome AF: 0.382 AC: 58124 AN: 152016 Hom.: 11463 Cov.: 32 AF XY: 0.387 AC XY: 28745 AN XY: 74322

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.402

Alfa AF: 0.381 Hom.: 23256

Bravo AF: 0.398

TwinsUK AF: 0.328 AC: 1217

ALSPAC AF: 0.344 AC: 1326

ESP6500AA AF: 0.323 AC: 447

ESP6500EA AF: 0.362 AC: 1151

Asia WGS AF: 0.463 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.68	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	4.6
DANN	Benign	0.52
FATHMM_MKL	Benign	0.31	N
MetaRNN	Benign	0.0017	T
Vest4		0.11
MVP		0.28
GERP RS		4.5

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

Publications

LitVar

Other links and lift over

dbSNP: rs2269650; hg19: chr1-175129691; COSMIC: COSV70593800; COSMIC: COSV70593800;