21-39694299-A-G

Variant names:

• chr21-39694299-A-G
• rs2837121
• ENST00000416555.1:n.221-28177A>G

Variant summary

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

The ENST00000416555.1(ENSG00000225330):​n.221-28177A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,980 control chromosomes in the GnomAD database, including 14,697 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 0.42 (14697 hom., cov: 32)
• Consequence: ENSG00000225330 ENST00000416555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 5 publications found

Genes affected

ENSG00000225330 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416555.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225330	ENST00000416555.1	TSL:3	n.221-28177A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64528 AN: 151862 Hom.: 14693 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.425 AC: 64559 AN: 151980 Hom.: 14697 Cov.: 32 AF XY: 0.420 AC XY: 31167 AN XY: 74292

African (AFR) AF: 0.295 AC: 12219 AN: 41450

American (AMR) AF: 0.483 AC: 7370 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.149 AC: 770 AN: 5160

South Asian (SAS) AF: 0.394 AC: 1892 AN: 4806

European-Finnish (FIN) AF: 0.412 AC: 4356 AN: 10564

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34636 AN: 67952

Other (OTH) AF: 0.455 AC: 960 AN: 2112

Alfa AF: 0.499 Hom.: 30517

Bravo AF: 0.427

Asia WGS AF: 0.295 AC: 1024 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.0
DANN	Benign	0.82
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2837121; hg19: chr21-41066226;