1-45304495-G-C

Variant names:

• chr1-45304495-G-C
• rs11576668
• ENST00000626198.1:n.586G>C

Variant summary

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

The ENST00000626198.1(LINC01144):​n.586G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,530 control chromosomes in the GnomAD database, including 434 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 0.068 (434 hom., cov: 31)
  • Exomes 𝑓: 0.030 (0 hom.)
• Consequence: LINC01144 ENST00000626198.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 4 publications found

Genes affected

LINC01144 (HGNC:49460): (long intergenic non-protein coding RNA 1144)

ZSWIM5 (HGNC:29299): (zinc finger SWIM-type containing 5) Predicted to enable zinc ion binding activity. Located in extracellular space. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626198.1. 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
	LINC01144	NR_024270.1		n.586G>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01144	ENST00000626198.1	TSL:6	n.586G>C		non_coding_transcript_exon	Exon 1 of 1
	ZSWIM5	ENST00000464588.1	TSL:3	n.97-438C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10281 AN: 152076 Hom.: 434 Cov.: 31

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.0676

GnomAD4 exome AF: 0.0298 AC: 10 AN: 336 Hom.: 0 Cov.: 0 AF XY: 0.0368 AC XY: 10 AN XY: 272

African (AFR) AF: 0.00 AC: 0 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.167 AC: 1 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0319 AC: 9 AN: 282

Other (OTH) AF: 0.00 AC: 0 AN: 12

GnomAD4 genome AF: 0.0676 AC: 10283 AN: 152194 Hom.: 434 Cov.: 31 AF XY: 0.0665 AC XY: 4948 AN XY: 74400

African (AFR) AF: 0.0351 AC: 1459 AN: 41544

American (AMR) AF: 0.0457 AC: 698 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0661 AC: 318 AN: 4812

European-Finnish (FIN) AF: 0.0867 AC: 920 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6445 AN: 67994

Other (OTH) AF: 0.0669 AC: 141 AN: 2108

Alfa AF: 0.0393 Hom.: 34

Bravo AF: 0.0626

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		0.051

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11576668; hg19: chr1-45770167;