rs2823322

Positions:

• chr21-15520713-G-A
• chr21-15520713-G-C

Variant summary

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

The ENST00000634644.1(ENSG00000229425):​n.355-6779C>T 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 0.225 in 152,080 control chromosomes in the GnomAD database, including 4,091 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 0.23 (4091 hom., cov: 32)
• Consequence: ENST00000634644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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
	ENST00000634644.1	n.355-6779C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34276 AN: 151962 Hom.: 4089 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.226 AC: 34294 AN: 152080 Hom.: 4091 Cov.: 32 AF XY: 0.226 AC XY: 16778 AN XY: 74332

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0783

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.253

Alfa AF: 0.102 Hom.: 143

Bravo AF: 0.234

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823322; hg19: chr21-16893032;