rs1057302

Positions:

• chr1-175157287-A-G
• chr1-175157287-A-T

Variant summary

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

The NM_014656.3(KIAA0040):​c.*3427T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,110 control chromosomes in the GnomAD database, including 11,210 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 0.37 (11207 hom., cov: 32)
  • Exomes 𝑓: 0.70 (3 hom.)
• Consequence: KIAA0040 NM_014656.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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 (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0040	NM_014656.3	c.*3427T>C		3_prime_UTR_variant	4/4	ENST00000423313.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0040	ENST00000423313.6	c.*3427T>C		3_prime_UTR_variant	4/4	1	NM_014656.3	P1
KIAA0040	ENST00000444639.5	c.*3427T>C		3_prime_UTR_variant	4/4	1		P1
KIAA0040	ENST00000619513.1	c.*2882T>C		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56427 AN: 151982 Hom.: 11203 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.0995

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 3 Cov.: 0 AF XY: 0.625 AC XY: 5 AN XY: 8

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.371 AC: 56448 AN: 152100 Hom.: 11207 Cov.: 32 AF XY: 0.369 AC XY: 27467 AN XY: 74350

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.359

Alfa AF: 0.367 Hom.: 2361

Bravo AF: 0.351

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.50

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: rs1057302; hg19: chr1-175126423;