chr21-39694299-A-G

Position:

• chr21-39694299-A-G

Variant summary

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

The ENST00000416555.1(ENSG00000225330):​n.221-28177A>G variant causes a intron, non coding transcript 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: ENST00000416555.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000416555.1	n.221-28177A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.455

Alfa AF: 0.501 Hom.: 25773

Bravo AF: 0.427

Asia WGS AF: 0.295 AC: 1024 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2837121; hg19: chr21-41066226;