rs1852579

Variant names:

• chr6-71387981-T-A
• rs1852579
• ENST00000624429.1:n.2849A>T

Variant summary

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

The ENST00000624429.1(ENSG00000279289):​n.2849A>T 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 0.0808 in 152,164 control chromosomes in the GnomAD database, including 757 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 0.081 (757 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000279289 ENST00000624429.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 1 publications found

Genes affected

ENSG00000279289 (HGNC:):

LINC00472 (HGNC:21380): (long intergenic non-protein coding RNA 472)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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
ENSG00000279289	ENST00000624429.1	n.2849A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00472	ENST00000413945.6	n.344+28429A>T		intron_variant	Intron 3 of 3	3
LINC00472	ENST00000436803.6	n.479+28429A>T		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12281 AN: 152046 Hom.: 757 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.0679

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0808 AC: 12295 AN: 152164 Hom.: 757 Cov.: 32 AF XY: 0.0787 AC XY: 5853 AN XY: 74410

African (AFR) AF: 0.173 AC: 7154 AN: 41454

American (AMR) AF: 0.0411 AC: 628 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0242 AC: 117 AN: 4832

European-Finnish (FIN) AF: 0.0486 AC: 516 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0516 AC: 3510 AN: 68006

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0692 Hom.: 63

Bravo AF: 0.0848

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1852579; hg19: chr6-72097684;