21-19594402-A-G

Variant names:

• chr21-19594402-A-G
• rs2825673
• ENST00000763543.1:n.975A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000763543.1(ENSG00000299439):​n.975A>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 0.201 in 151,986 control chromosomes in the GnomAD database, including 3,813 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 0.20 (3813 hom., cov: 32)
• Consequence: ENSG00000299439 ENST00000763543.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

Genes affected

ENSG00000299439 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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
ENSG00000299439	ENST00000763543.1	n.975A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000299439	ENST00000763544.1	n.642A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30486 AN: 151868 Hom.: 3816 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30519 AN: 151986 Hom.: 3813 Cov.: 32 AF XY: 0.200 AC XY: 14895 AN XY: 74298

African (AFR) AF: 0.343 AC: 14217 AN: 41414

American (AMR) AF: 0.128 AC: 1950 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3472

East Asian (EAS) AF: 0.246 AC: 1265 AN: 5144

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4828

European-Finnish (FIN) AF: 0.140 AC: 1477 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9092 AN: 67970

Other (OTH) AF: 0.199 AC: 421 AN: 2114

Alfa AF: 0.155 Hom.: 4951

Bravo AF: 0.205

Asia WGS AF: 0.234 AC: 812 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.70
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2825673; hg19: chr21-20966716;