rs6733000

Variant names:

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

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​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: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 0 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435237.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231204	ENST00000435237.1	TSL:3	n.194-70025C>T		intron	N/A
	ENSG00000231204	ENST00000717099.1		n.556-70025C>T		intron	N/A
	ENSG00000231204	ENST00000753412.1		n.187+1743C>T		intron	N/A

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

African (AFR) AF: 0.163 AC: 6750 AN: 41484

American (AMR) AF: 0.0961 AC: 1467 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3464

East Asian (EAS) AF: 0.0344 AC: 176 AN: 5120

South Asian (SAS) AF: 0.0557 AC: 269 AN: 4828

European-Finnish (FIN) AF: 0.0567 AC: 602 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0819 AC: 5565 AN: 67942

Other (OTH) AF: 0.110 AC: 233 AN: 2110

Alfa AF: 0.0862 Hom.: 331

Bravo AF: 0.109

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.45
PhyloP100		0.0050

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6733000;

hg19: chr2-21952204;