rs2834072

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000227757 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000227757	ENST00000454622.2	n.201+32748T>C		intron_variant	Intron 1 of 1	2

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

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.455

Alfa AF: 0.456 Hom.: 34352

Bravo AF: 0.486

Asia WGS AF: 0.440 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2834072; hg19: chr21-34410464;