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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372740	XR_001755096.1	n.1268-523C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303199	ENST00000792651.1	n.335-523C>T		intron_variant	Intron 2 of 2
ENSG00000303199	ENST00000792655.1	n.336-523C>T		intron_variant	Intron 2 of 2
ENSG00000303199	ENST00000792656.1	n.235-523C>T		intron_variant	Intron 3 of 3

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 = 0.000000), 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 v4.3

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

Other links and lift over

dbSNP: rs1297533; hg19: chr21-18383162;