21-29190676-A-T

Variant names:

• chr21-29190676-A-T
• rs2832253
• ENST00000801811.1:n.98-8446T>A

Variant summary

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

The ENST00000801811.1(ENSG00000224649):​n.98-8446T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,292 control chromosomes in the GnomAD database, including 471 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 0.068 (471 hom., cov: 33)
• Consequence: ENSG00000224649 ENST00000801811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 1 publications found

Genes affected

ENSG00000224649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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
ENSG00000224649	ENST00000801811.1	n.98-8446T>A		intron_variant	Intron 1 of 1
ENSG00000224649	ENST00000801812.1	n.98-2882T>A		intron_variant	Intron 1 of 2
ENSG00000224649	ENST00000801814.1	n.292-2882T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10356 AN: 152174 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0680 AC: 10353 AN: 152292 Hom.: 471 Cov.: 33 AF XY: 0.0649 AC XY: 4833 AN XY: 74468

African (AFR) AF: 0.0204 AC: 848 AN: 41560

American (AMR) AF: 0.0558 AC: 854 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4826

European-Finnish (FIN) AF: 0.0762 AC: 808 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6986 AN: 68014

Other (OTH) AF: 0.0799 AC: 169 AN: 2116

Alfa AF: 0.0410 Hom.: 32

Bravo AF: 0.0644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2832253; hg19: chr21-30562997;