6-12485931-T-G

Variant names:

• chr6-12485931-T-G
• rs9296397
• ENST00000723024.1:n.730A>C

Variant summary

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

The ENST00000723024.1(ENSG00000294347):​n.730A>C 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 0.0424 in 152,250 control chromosomes in the GnomAD database, including 294 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 0.042 (294 hom., cov: 32)
• Consequence: ENSG00000294347 ENST00000723024.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546
• Publications: 0 publications found

Genes affected

ENSG00000294347 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294347	ENST00000723024.1		n.730A>C		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000294347	ENST00000723025.1		n.798A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000294347	ENST00000723026.1		n.780A>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6442 AN: 152132 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0424 AC: 6455 AN: 152250 Hom.: 294 Cov.: 32 AF XY: 0.0422 AC XY: 3138 AN XY: 74448

African (AFR) AF: 0.115 AC: 4793 AN: 41534

American (AMR) AF: 0.0247 AC: 378 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4826

European-Finnish (FIN) AF: 0.00574 AC: 61 AN: 10626

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 777 AN: 68010

Other (OTH) AF: 0.0475 AC: 100 AN: 2106

Alfa AF: 0.0488 Hom.: 136

Bravo AF: 0.0451

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs9296397; hg19: chr6-12486163;