rs7236133

Variant names:

• chr18-61726757-G-A
• rs7236133
• ENST00000590199.6:n.537+21283C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-61726757-G-A
• chr18-61726757-G-T

Variant summary

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

The ENST00000590199.6(ENSG00000267175):​n.537+21283C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0672 in 152,096 control chromosomes in the GnomAD database, including 1,122 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 0.067 (1122 hom., cov: 32)
• Consequence: ENSG00000267175 ENST00000590199.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 0 publications found

Genes affected

ENSG00000267175 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590199.6. 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
	ENSG00000267175	ENST00000590199.6	TSL:3	n.537+21283C>T		intron	N/A
	ENSG00000267175	ENST00000590968.1	TSL:2	n.233+21318C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 10171 AN: 151978 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00359

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00278

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0672 AC: 10214 AN: 152096 Hom.: 1122 Cov.: 32 AF XY: 0.0642 AC XY: 4777 AN XY: 74358

African (AFR) AF: 0.229 AC: 9483 AN: 41444

American (AMR) AF: 0.0248 AC: 379 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4816

European-Finnish (FIN) AF: 0.00359 AC: 38 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00278 AC: 189 AN: 68008

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0451 Hom.: 108

Bravo AF: 0.0772

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.93
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7236133; hg19: chr18-59393990;