ENST00000673788.2:n.381+1006G>A

Variant names:

• chr21-14723270-C-T
• rs2822877
• ENST00000673788.2:n.381+1006G>A

Variant summary

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

The ENST00000673788.2(ENSG00000232884):​n.381+1006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,032 control chromosomes in the GnomAD database, including 3,857 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 0.21 (3857 hom., cov: 32)
• Consequence: ENSG00000232884 ENST00000673788.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 1 publications found

Genes affected

ENSG00000232884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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
ENSG00000232884	ENST00000673788.2	n.381+1006G>A		intron_variant	Intron 3 of 3
ENSG00000232884	ENST00000700842.1	n.288+16983G>A		intron_variant	Intron 2 of 2
ENSG00000232884	ENST00000806529.1	n.302+39568G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32655 AN: 151914 Hom.: 3856 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.215 AC: 32660 AN: 152032 Hom.: 3857 Cov.: 32 AF XY: 0.212 AC XY: 15772 AN XY: 74290

African (AFR) AF: 0.146 AC: 6058 AN: 41460

American (AMR) AF: 0.162 AC: 2476 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.124 AC: 641 AN: 5174

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4820

European-Finnish (FIN) AF: 0.255 AC: 2696 AN: 10558

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17837 AN: 67960

Other (OTH) AF: 0.214 AC: 452 AN: 2112

Alfa AF: 0.229 Hom.: 536

Bravo AF: 0.205

Asia WGS AF: 0.197 AC: 685 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	0.79
DANN	Benign	0.26
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs2822877; hg19: chr21-16095591;