6-32893839-G-T

Position:

• chr6-32893839-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688327.2(ENSG00000289559):​n.827C>A 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 0.351 in 151,876 control chromosomes in the GnomAD database, including 9,504 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 0.35 (9504 hom., cov: 32)
• Consequence: ENSG00000289559 ENST00000688327.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

Genes affected

ENSG00000289559 (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 (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32893839G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289559	ENST00000688327.2	n.827C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53269 AN: 151760 Hom.: 9507 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.351 AC: 53273 AN: 151876 Hom.: 9504 Cov.: 32 AF XY: 0.346 AC XY: 25693 AN XY: 74264

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.355

Alfa AF: 0.217 Hom.: 466

Bravo AF: 0.351

Asia WGS AF: 0.304 AC: 1059 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	0.67
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs241412; hg19: chr6-32861616;