21-14711202-A-G

Variant names:

• chr21-14711202-A-G
• rs2822859
• ENST00000673788.2:n.381+13074T>C

Variant summary

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

The ENST00000673788.2(ENSG00000232884):​n.381+13074T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,006 control chromosomes in the GnomAD database, including 11,763 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 0.39 (11763 hom., cov: 32)
• Consequence: ENSG00000232884 ENST00000673788.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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+13074T>C		intron_variant	Intron 3 of 3
ENSG00000232884	ENST00000700842.1	n.288+29051T>C		intron_variant	Intron 2 of 2
ENSG00000232884	ENST00000806529.1	n.303-34122T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59709 AN: 151886 Hom.: 11745 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.393 AC: 59763 AN: 152006 Hom.: 11763 Cov.: 32 AF XY: 0.392 AC XY: 29166 AN XY: 74316

African (AFR) AF: 0.404 AC: 16726 AN: 41422

American (AMR) AF: 0.337 AC: 5156 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2600 AN: 5150

South Asian (SAS) AF: 0.365 AC: 1764 AN: 4828

European-Finnish (FIN) AF: 0.405 AC: 4293 AN: 10592

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26739 AN: 67952

Other (OTH) AF: 0.400 AC: 844 AN: 2110

Alfa AF: 0.254 Hom.: 794

Bravo AF: 0.392

Asia WGS AF: 0.444 AC: 1540 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.42
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2822859; hg19: chr21-16083523;