rs1297533

Variant names:

• chr21-17010843-G-A
• rs1297533
• ENST00000792651.1:n.335-523C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000792651.1(ENSG00000303199):​n.335-523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00020 (0 hom., cov: 25)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000303199 ENST00000792651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 3 publications found

Genes affected

ENSG00000303199 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792651.1. 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
	ENSG00000303199	ENST00000792651.1		n.335-523C>T		intron	N/A
	ENSG00000303199	ENST00000792655.1		n.336-523C>T		intron	N/A
	ENSG00000303199	ENST00000792656.1		n.235-523C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000196 AC: 21 AN: 107128 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.0000653

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000402

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000160

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000242

Gnomad OTH AF: 0.00133

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000196 AC: 21 AN: 107226 Hom.: 0 Cov.: 25 AF XY: 0.000156 AC XY: 8 AN XY: 51174

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000651 AC: 2 AN: 30728

American (AMR) AF: 0.000402 AC: 4 AN: 9962

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2530

East Asian (EAS) AF: 0.00 AC: 0 AN: 3066

South Asian (SAS) AF: 0.00 AC: 0 AN: 2790

European-Finnish (FIN) AF: 0.000160 AC: 1 AN: 6244

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 190

European-Non Finnish (NFE) AF: 0.000242 AC: 12 AN: 49502

Other (OTH) AF: 0.00132 AC: 2 AN: 1516

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000337 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.43
PhyloP100		-0.86

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: rs1297533;

hg19: chr21-18383162;