21-33902813-G-T

Variant names:

• chr21-33902813-G-T
• rs731059
• ENST00000429238.2:c.441+4528C>A

Variant summary

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

The ENST00000429238.2(ENSG00000249209):​c.441+4528C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,084 control chromosomes in the GnomAD database, including 7,843 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 0.32 (7843 hom., cov: 32)
• Consequence: ENSG00000249209 ENST00000429238.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

ENSG00000249209 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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
ENSG00000249209	ENST00000429238.2	c.441+4528C>A		intron_variant	Intron 6 of 7	5		ENSP00000394107.2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48612 AN: 151964 Hom.: 7841 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.320 AC: 48636 AN: 152084 Hom.: 7843 Cov.: 32 AF XY: 0.320 AC XY: 23782 AN XY: 74332

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.287

Alfa AF: 0.296 Hom.: 12724

Bravo AF: 0.318

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs731059; hg19: chr21-35275117;