6-23472836-A-G

Variant names:

• chr6-23472836-A-G
• rs199076
• ENST00000690652.3:n.356-15166T>C

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.356-15166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 141,382 control chromosomes in the GnomAD database, including 1,866 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 0.16 (1866 hom., cov: 30)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 4 publications found

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690652.3. 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
	ENSG00000289368	ENST00000690652.3		n.356-15166T>C		intron	N/A
	ENSG00000289368	ENST00000700866.2		n.181-15166T>C		intron	N/A
	ENSG00000289368	ENST00000702216.2		n.203-15166T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 21912 AN: 141380 Hom.: 1862 Cov.: 30

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.198

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.155 AC: 21921 AN: 141382 Hom.: 1866 Cov.: 30 AF XY: 0.157 AC XY: 10722 AN XY: 68424

African (AFR) AF: 0.213 AC: 8409 AN: 39566

American (AMR) AF: 0.163 AC: 2093 AN: 12858

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 416 AN: 3332

East Asian (EAS) AF: 0.302 AC: 1372 AN: 4546

South Asian (SAS) AF: 0.181 AC: 786 AN: 4342

European-Finnish (FIN) AF: 0.130 AC: 1077 AN: 8286

Middle Eastern (MID) AF: 0.204 AC: 55 AN: 270

European-Non Finnish (NFE) AF: 0.110 AC: 7208 AN: 65352

Other (OTH) AF: 0.166 AC: 320 AN: 1924

Alfa AF: 0.135 Hom.: 187

Bravo AF: 0.157

Asia WGS AF: 0.232 AC: 780 AN: 3352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs199076; hg19: chr6-23473064;