21-25316569-A-T

Position:

• chr21-25316569-A-T

Variant summary

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

The ENST00000656005.1(ENSG00000222042):​n.217+44619T>A 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 0.501 in 152,090 control chromosomes in the GnomAD database, including 20,435 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 0.50 (20435 hom., cov: 33)
• Consequence: ENST00000656005.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656005.1	n.217+44619T>A		intron_variant, non_coding_transcript_variant
	ENST00000409758.1	n.89+17168T>A		intron_variant, non_coding_transcript_variant		3
	ENST00000667825.1	n.189+44619T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76058 AN: 151972 Hom.: 20396 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.501 AC: 76148 AN: 152090 Hom.: 20435 Cov.: 33 AF XY: 0.499 AC XY: 37064 AN XY: 74344

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.453

Alfa AF: 0.459 Hom.: 2086

Bravo AF: 0.518

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716195; hg19: chr21-26688883;