NM_020776.3:c.*3004C>T

Variant names:

• chr18-37225231-C-T
• rs2017027
• NM_020776.3:c.*3004C>T

Variant summary

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

The NM_020776.3(KIAA1328):​c.*3004C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 985,326 control chromosomes in the GnomAD database, including 8,688 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 0.11 (1085 hom., cov: 32)
  • Exomes 𝑓: 0.13 (7603 hom.)
• Consequence: KIAA1328 NM_020776.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 7 publications found

Genes affected

KIAA1328 (HGNC:29248): (KIAA1328)

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 (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1328	NM_020776.3	c.*3004C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000280020.10	NP_065827.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1328	ENST00000280020.10	c.*3004C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_020776.3	ENSP00000280020.5
KIAA1328	ENST00000591619.5	c.*3004C>T		3_prime_UTR_variant	Exon 10 of 11	1		ENSP00000465550.1
KIAA1328	ENST00000592611.5	n.*1283+3114C>T		intron_variant	Intron 9 of 10	2		ENSP00000468653.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16214 AN: 152120 Hom.: 1084 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.134 AC: 111319 AN: 833088 Hom.: 7603 Cov.: 31 AF XY: 0.134 AC XY: 51694 AN XY: 384714

African (AFR) AF: 0.0207 AC: 327 AN: 15786

American (AMR) AF: 0.111 AC: 109 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 992 AN: 5152

East Asian (EAS) AF: 0.113 AC: 411 AN: 3630

South Asian (SAS) AF: 0.115 AC: 1886 AN: 16458

European-Finnish (FIN) AF: 0.174 AC: 49 AN: 282

Middle Eastern (MID) AF: 0.109 AC: 177 AN: 1622

European-Non Finnish (NFE) AF: 0.136 AC: 103770 AN: 761878

Other (OTH) AF: 0.132 AC: 3598 AN: 27296

GnomAD4 genome AF: 0.106 AC: 16206 AN: 152238 Hom.: 1085 Cov.: 32 AF XY: 0.108 AC XY: 8074 AN XY: 74436

African (AFR) AF: 0.0319 AC: 1327 AN: 41568

American (AMR) AF: 0.118 AC: 1808 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 678 AN: 3468

East Asian (EAS) AF: 0.129 AC: 666 AN: 5174

South Asian (SAS) AF: 0.109 AC: 527 AN: 4824

European-Finnish (FIN) AF: 0.157 AC: 1662 AN: 10592

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9107 AN: 67990

Other (OTH) AF: 0.111 AC: 234 AN: 2116

Alfa AF: 0.122 Hom.: 724

Bravo AF: 0.101

Asia WGS AF: 0.131 AC: 458 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	1.8
DANN	Benign	0.56
PhyloP100		0.43
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: rs2017027; hg19: chr18-34805194;