chr21-33038156-A-G

Variant names:

• chr21-33038156-A-G
• rs2834072
• ENST00000454622.2:n.201+32748T>C

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.201+32748T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,004 control chromosomes in the GnomAD database, including 18,686 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 0.49 (18686 hom., cov: 32)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.59
• Publications: 15 publications found

Genes affected

ENSG00000227757 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454622.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227757	ENST00000454622.2	TSL:2	n.201+32748T>C		intron	N/A
	ENSG00000227757	ENST00000777421.1		n.91+32748T>C		intron	N/A
	ENSG00000227757	ENST00000777422.1		n.108-15230T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74559 AN: 151886 Hom.: 18663 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.491 AC: 74631 AN: 152004 Hom.: 18686 Cov.: 32 AF XY: 0.493 AC XY: 36625 AN XY: 74304

African (AFR) AF: 0.570 AC: 23627 AN: 41428

American (AMR) AF: 0.457 AC: 6983 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3464

East Asian (EAS) AF: 0.340 AC: 1762 AN: 5188

South Asian (SAS) AF: 0.453 AC: 2180 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5703 AN: 10534

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31071 AN: 67976

Other (OTH) AF: 0.455 AC: 960 AN: 2108

Alfa AF: 0.462 Hom.: 75033

Bravo AF: 0.486

Asia WGS AF: 0.440 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.23
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs2834072; hg19: chr21-34410464;