21-24046613-G-C

Variant names:

• chr21-24046613-G-C
• rs2828759
• ENST00000434859.1:n.81-2907G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434859.1(ENSG00000226996):​n.81-2907G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,766 control chromosomes in the GnomAD database, including 33,386 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 0.66 (33386 hom., cov: 30)
• Consequence: ENSG00000226996 ENST00000434859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

ENSG00000226996 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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
ENSG00000226996	ENST00000434859.1	n.81-2907G>C		intron_variant	Intron 1 of 1	3
ENSG00000287801	ENST00000668921.1	n.138-61607C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100444 AN: 151648 Hom.: 33349 Cov.: 30

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.662 AC: 100533 AN: 151766 Hom.: 33386 Cov.: 30 AF XY: 0.663 AC XY: 49142 AN XY: 74164

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.646

Alfa AF: 0.662 Hom.: 3941

Bravo AF: 0.657

Asia WGS AF: 0.666 AC: 2308 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.87
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2828759; hg19: chr21-25418928;