chr1-175157709-T-C

Variant names:

• chr1-175157709-T-C
• rs1057285
• NM_014656.3:c.*3005A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.84).
• 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 rank	MANE	Protein	UniProt
KIAA0040	NM_014656.3	c.*3005A>G		3_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.*3005A>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_014656.3	ENSP00000462172.1
KIAA0040	ENST00000444639.5	c.*3005A>G		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000463734.1
KIAA0040	ENST00000619513.1	c.*2460A>G		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000478803.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 4 AN: 12

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.250 AC: 10317 AN: 41288

American (AMR) AF: 0.146 AC: 2229 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1714 AN: 5108

South Asian (SAS) AF: 0.275 AC: 1301 AN: 4734

European-Finnish (FIN) AF: 0.124 AC: 1300 AN: 10524

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9763 AN: 67814

Other (OTH) AF: 0.187 AC: 394 AN: 2112

Alfa AF: 0.159 Hom.: 1218

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
PhyloP100		0.53
Mutation Taster		=100/0	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: rs1057285; hg19: chr1-175126845;