21-23438877-C-G

Variant names:

• chr21-23438877-C-G
• rs2828151
• ENST00000797133.1:n.644+29669C>G

Variant summary

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

The ENST00000797133.1(ENSG00000227716):​n.644+29669C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,568 control chromosomes in the GnomAD database, including 19,577 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 0.50 (19577 hom., cov: 31)
• Consequence: ENSG00000227716 ENST00000797133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

Genes affected

ENSG00000227716 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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
ENSG00000227716	ENST00000797133.1	n.644+29669C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 75987 AN: 151450 Hom.: 19568 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.502 AC: 76025 AN: 151568 Hom.: 19577 Cov.: 31 AF XY: 0.503 AC XY: 37237 AN XY: 74082

African (AFR) AF: 0.403 AC: 16646 AN: 41344

American (AMR) AF: 0.430 AC: 6535 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 1999 AN: 3462

East Asian (EAS) AF: 0.421 AC: 2169 AN: 5156

South Asian (SAS) AF: 0.592 AC: 2849 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5721 AN: 10526

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38323 AN: 67744

Other (OTH) AF: 0.499 AC: 1051 AN: 2108

Alfa AF: 0.396 Hom.: 1073

Bravo AF: 0.485

Asia WGS AF: 0.473 AC: 1640 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.43
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2828151; hg19: chr21-24811197;