6-23557933-G-A

Variant names:

• chr6-23557933-G-A
• rs199131
• ENST00000690652.3:n.355+26171C>T

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.355+26171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,948 control chromosomes in the GnomAD database, including 2,595 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 0.11 (2595 hom., cov: 31)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 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.355+26171C>T		intron	N/A
	ENSG00000289368	ENST00000700866.2		n.180+26171C>T		intron	N/A
	ENSG00000289368	ENST00000700904.2		n.201-12576C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17119 AN: 151830 Hom.: 2586 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00387

Gnomad SAS AF: 0.0185

Gnomad FIN AF: 0.00623

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0199

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.113 AC: 17172 AN: 151948 Hom.: 2595 Cov.: 31 AF XY: 0.110 AC XY: 8166 AN XY: 74288

African (AFR) AF: 0.349 AC: 14428 AN: 41396

American (AMR) AF: 0.0615 AC: 939 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3466

East Asian (EAS) AF: 0.00388 AC: 20 AN: 5152

South Asian (SAS) AF: 0.0181 AC: 87 AN: 4808

European-Finnish (FIN) AF: 0.00623 AC: 66 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0199 AC: 1352 AN: 67964

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0709 Hom.: 188

Bravo AF: 0.127

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs199131; hg19: chr6-23558161;