rs1852579

Positions:

• chr6-71387981-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000279289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.71387981T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279289	ENST00000624429.1	n.2849A>T		non_coding_transcript_exon_variant	1/1	6
LINC00472	ENST00000413945.6	n.344+28429A>T		intron_variant		3
LINC00472	ENST00000436803.6	n.479+28429A>T		intron_variant		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

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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0516

Gnomad4 OTH AF: 0.0672

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1852579; hg19: chr6-72097684;