21-36580889-A-G

Position:

• chr21-36580889-A-G

Variant summary

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

The ENST00000660763.1(ENSG00000286852):​n.477A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,974 control chromosomes in the GnomAD database, including 22,630 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 0.54 (22630 hom., cov: 32)
• Consequence: ENSG00000286852 ENST00000660763.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

Genes affected

ENSG00000286852 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36580889A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286852	ENST00000660763.1	n.477A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81548 AN: 151856 Hom.: 22622 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.537 AC: 81596 AN: 151974 Hom.: 22630 Cov.: 32 AF XY: 0.534 AC XY: 39668 AN XY: 74292

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.555

Alfa AF: 0.605 Hom.: 55408

Bravo AF: 0.528

Asia WGS AF: 0.527 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs432137; hg19: chr21-37953187;