rs1220398

Variant names:

• chr1-9934281-A-G
• rs1220398
• NM_032368.5:c.336+481T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-9934281-A-G
• chr1-9934281-A-T

Variant summary

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

The NM_032368.5(LZIC):​c.336+481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,900 control chromosomes in the GnomAD database, including 44,147 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 0.74 (44147 hom., cov: 30)
• Consequence: LZIC NM_032368.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 6 publications found

Genes affected

LZIC (HGNC:17497): (leucine zipper and CTNNBIP1 domain containing) Predicted to enable beta-catenin binding activity. Predicted to be involved in response to ionizing radiation. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000228150 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032368.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LZIC	NM_032368.5	MANE Select	c.336+481T>C		intron	N/A	NP_115744.2
	LZIC	NM_001316974.2		c.399+481T>C		intron	N/A	NP_001303903.1
	LZIC	NM_001316975.2		c.336+481T>C		intron	N/A	NP_001303904.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LZIC	ENST00000377223.6	TSL:1 MANE Select	c.336+481T>C		intron	N/A	ENSP00000366430.1
	LZIC	ENST00000377213.1	TSL:1	c.336+481T>C		intron	N/A	ENSP00000366418.1
	LZIC	ENST00000400903.6	TSL:1	c.336+481T>C		intron	N/A	ENSP00000383695.2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112888 AN: 151786 Hom.: 44133 Cov.: 30

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.780

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.744 AC: 112939 AN: 151900 Hom.: 44147 Cov.: 30 AF XY: 0.744 AC XY: 55261 AN XY: 74240

African (AFR) AF: 0.487 AC: 20176 AN: 41410

American (AMR) AF: 0.874 AC: 13311 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3345 AN: 5164

South Asian (SAS) AF: 0.675 AC: 3245 AN: 4806

European-Finnish (FIN) AF: 0.820 AC: 8633 AN: 10522

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58858 AN: 67986

Other (OTH) AF: 0.774 AC: 1631 AN: 2108

Alfa AF: 0.795 Hom.: 64828

Bravo AF: 0.737

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.7
DANN	Benign	0.76
PhyloP100		0.090
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: rs1220398; hg19: chr1-9994339;