6-32893839-G-T

Variant names:

• chr6-32893839-G-T
• rs241412
• ENST00000688327.3:n.867C>A

Variant summary

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

The ENST00000688327.3(ENSG00000289559):​n.867C>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 ENST00000688327.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 7 publications found

Genes affected

ENSG00000289559 (HGNC:):

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688327.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289559	ENST00000688327.3		n.867C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289559	ENST00000753352.1		n.738+60C>A		intron	N/A
	ENSG00000289559	ENST00000753353.1		n.390-135C>A		intron	N/A

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

African (AFR) AF: 0.307 AC: 12707 AN: 41426

American (AMR) AF: 0.352 AC: 5377 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1025 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1651 AN: 5154

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4820

European-Finnish (FIN) AF: 0.363 AC: 3837 AN: 10562

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26131 AN: 67854

Other (OTH) AF: 0.355 AC: 748 AN: 2108

Alfa AF: 0.269 Hom.: 1186

Bravo AF: 0.351

Asia WGS AF: 0.304 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs241412; hg19: chr6-32861616;