21-33920895-T-G

Position:

• chr21-33920895-T-G

Variant summary

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

The ENST00000429238.2(ENSG00000249209):​c.-214-4918A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 152,232 control chromosomes in the GnomAD database, including 498 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 0.078 (498 hom., cov: 31)
• Consequence: ENSG00000249209 ENST00000429238.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

Genes affected

ENSG00000249209 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33920895T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249209	ENST00000429238.2	c.-214-4918A>C		intron_variant		5		ENSP00000394107.2

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11835 AN: 152114 Hom.: 499 Cov.: 31

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0779 AC: 11856 AN: 152232 Hom.: 498 Cov.: 31 AF XY: 0.0749 AC XY: 5573 AN XY: 74450

Gnomad4 AFR AF: 0.0712

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00579

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0933

Gnomad4 OTH AF: 0.0838

Alfa AF: 0.0922 Hom.: 884

Bravo AF: 0.0789

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.79

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: rs12482697; hg19: chr21-35293199;