chr1-175157709-T-C

Position:

• chr1-175157709-T-C

Variant summary

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

The NM_014656.3(KIAA0040):​c.*3005A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,492 control chromosomes in the GnomAD database, including 2,877 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 0.18 (2875 hom., cov: 31)
  • Exomes 𝑓: 0.43 (2 hom.)
• Consequence: KIAA0040 NM_014656.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0040	NM_014656.3	c.*3005A>G		3_prime_UTR_variant	4/4	ENST00000423313.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0040	ENST00000423313.6	c.*3005A>G		3_prime_UTR_variant	4/4	1	NM_014656.3	P1
KIAA0040	ENST00000444639.5	c.*3005A>G		3_prime_UTR_variant	4/4	1		P1
KIAA0040	ENST00000619513.1	c.*2460A>G		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27716 AN: 151360 Hom.: 2865 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0996

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 6 AN XY: 12

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.183 AC: 27744 AN: 151478 Hom.: 2875 Cov.: 31 AF XY: 0.184 AC XY: 13598 AN XY: 73980

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.187

Alfa AF: 0.160 Hom.: 1108

Bravo AF: 0.187

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.37

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: rs1057285; hg19: chr1-175126845;