chr1-182149187-T-C

Variant names:

• chr1-182149187-T-C
• rs4451518
• ENST00000757631.1:n.172A>G

Variant summary

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

The ENST00000757631.1(ENSG00000298728):​n.172A>G 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 0.0402 in 152,290 control chromosomes in the GnomAD database, including 233 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 0.040 (233 hom., cov: 31)
• Consequence: ENSG00000298728 ENST00000757631.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 3 publications found

Genes affected

ENSG00000298728 (HGNC:):

LINC01344 (HGNC:50554): (long intergenic non-protein coding RNA 1344)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298728	ENST00000757631.1	n.172A>G		non_coding_transcript_exon_variant	Exon 1 of 1
LINC01344	ENST00000449842.2	n.770+17899A>G		intron_variant	Intron 4 of 4	3
LINC01344	ENST00000608183.1	n.1913+4537A>G		intron_variant	Intron 10 of 16	2

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6127 AN: 152170 Hom.: 233 Cov.: 31

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0402 AC: 6121 AN: 152290 Hom.: 233 Cov.: 31 AF XY: 0.0442 AC XY: 3288 AN XY: 74454

African (AFR) AF: 0.0143 AC: 593 AN: 41568

American (AMR) AF: 0.0410 AC: 627 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.193 AC: 998 AN: 5170

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1125 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0339 AC: 2304 AN: 68026

Other (OTH) AF: 0.0269 AC: 57 AN: 2116

Alfa AF: 0.0403 Hom.: 22

Bravo AF: 0.0365

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.76
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs4451518; hg19: chr1-182118322;