rs7236133

Variant names:

• chr18-61726757-G-A
• rs7236133
• ENST00000590199.5:n.190+21283C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000590968.1(ENSG00000267175):​n.233+21318C>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 ENST00000590968.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

ENSG00000267175 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267175	ENST00000590199.5	n.190+21283C>T		intron_variant	Intron 2 of 3	3
ENSG00000267175	ENST00000590968.1	n.233+21318C>T		intron_variant	Intron 2 of 3	2

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00359

Gnomad4 NFE AF: 0.00278

Gnomad4 OTH AF: 0.0511

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7236133; hg19: chr18-59393990;