21-21610512-A-T

Variant names:

• chr21-21610512-A-T
• rs10488908
• ENST00000428205.1:n.202-4518A>T

Variant summary

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

The ENST00000428205.1(ENSG00000234730):​n.202-4518A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0431 in 152,138 control chromosomes in the GnomAD database, including 234 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 0.043 (234 hom., cov: 32)
• Consequence: ENSG00000234730 ENST00000428205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 1 publications found

Genes affected

ENSG00000234730 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234730	ENST00000428205.1	TSL:2	n.202-4518A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0432 AC: 6564 AN: 152020 Hom.: 234 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0431 AC: 6560 AN: 152138 Hom.: 234 Cov.: 32 AF XY: 0.0405 AC XY: 3014 AN XY: 74352

African (AFR) AF: 0.0126 AC: 522 AN: 41554

American (AMR) AF: 0.0481 AC: 733 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3470

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5142

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4822

European-Finnish (FIN) AF: 0.0205 AC: 218 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4563 AN: 67960

Other (OTH) AF: 0.0562 AC: 119 AN: 2116

Alfa AF: 0.00881 Hom.: 2

Bravo AF: 0.0457

Asia WGS AF: 0.00808 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.83
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10488908; hg19: chr21-22982833;