rs1057239

Variant names:

• chr1-175161068-G-A
• rs1057239
• NM_014656.3:c.-55C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-175161068-G-A
• chr1-175161068-G-C
• chr1-175161068-G-T

Variant summary

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

The NM_014656.3(KIAA0040):​c.-55C>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 0.432 in 1,479,164 control chromosomes in the GnomAD database, including 142,773 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 (12917 hom., cov: 32)
  • Exomes 𝑓: 0.44 (129856 hom.)
• Consequence: KIAA0040 NM_014656.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 28 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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.-55C>T		5_prime_UTR_variant	Exon 4 of 4	ENST00000423313.6	NP_055471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0040	ENST00000423313.6	c.-55C>T		5_prime_UTR_variant	Exon 4 of 4	1	NM_014656.3	ENSP00000462172.1

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61626 AN: 151882 Hom.: 12920 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.393

GnomAD4 exome AF: 0.435 AC: 577592 AN: 1327162 Hom.: 129856 Cov.: 24 AF XY: 0.430 AC XY: 279789 AN XY: 650412

African (AFR) AF: 0.385 AC: 11253 AN: 29212

American (AMR) AF: 0.287 AC: 7740 AN: 26980

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 6338 AN: 21260

East Asian (EAS) AF: 0.131 AC: 4613 AN: 35226

South Asian (SAS) AF: 0.277 AC: 18875 AN: 68140

European-Finnish (FIN) AF: 0.455 AC: 21575 AN: 47386

Middle Eastern (MID) AF: 0.307 AC: 1183 AN: 3854

European-Non Finnish (NFE) AF: 0.465 AC: 483847 AN: 1040150

Other (OTH) AF: 0.403 AC: 22168 AN: 54954

GnomAD4 genome AF: 0.406 AC: 61647 AN: 152002 Hom.: 12917 Cov.: 32 AF XY: 0.402 AC XY: 29864 AN XY: 74298

African (AFR) AF: 0.393 AC: 16307 AN: 41454

American (AMR) AF: 0.342 AC: 5224 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3472

East Asian (EAS) AF: 0.131 AC: 677 AN: 5174

South Asian (SAS) AF: 0.271 AC: 1308 AN: 4818

European-Finnish (FIN) AF: 0.468 AC: 4932 AN: 10548

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

European-Non Finnish (NFE) AF: 0.455 AC: 30903 AN: 67952

Other (OTH) AF: 0.393 AC: 829 AN: 2108

Alfa AF: 0.420 Hom.: 39507

Bravo AF: 0.390

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.4
Mutation Taster		=300/0	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: rs1057239; hg19: chr1-175130204; COSMIC: COSV70594026;