rs9982023

chr21-28542904-A-G

Variant summary

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

The ENST00000433310.6(ENSG00000232855):n.456+34315T>C 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 0.123 in 152,066 control chromosomes in the GnomAD database, including 2,004 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 0.12 (2004 hom., cov: 31)
• Consequence: ENST00000433310.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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
	ENST00000433310.6	n.456+34315T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000430247.1	n.126+34371T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000659279.1	n.228+34249T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18661 AN: 151946 Hom.: 2001 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.123 AC: 18686 AN: 152066 Hom.: 2004 Cov.: 31 AF XY: 0.120 AC XY: 8895 AN XY: 74362

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.0132

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0428

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.104

Alfa AF: 0.103 Hom.: 224

Bravo AF: 0.131

Asia WGS AF: 0.0890 AC: 311 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	2.1
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9982023; hg19: chr21-29915226;