rs6733000

Variant names:

• chr2-21729332-C-T
• rs6733000
• ENST00000435237.1:n.194-70025C>T

Variant summary

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

The ENST00000435237.1(ENSG00000233005):​n.194-70025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,026 control chromosomes in the GnomAD database, including 937 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 0.10 (937 hom., cov: 32)
• Consequence: ENSG00000233005 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

ENSG00000233005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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
ENSG00000233005	ENST00000435237.1	n.194-70025C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15485 AN: 151908 Hom.: 928 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.102 AC: 15518 AN: 152026 Hom.: 937 Cov.: 32 AF XY: 0.0999 AC XY: 7426 AN XY: 74310

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0857 Hom.: 295

Bravo AF: 0.109

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733000; hg19: chr2-21952204;