rs2834467

chr21-34356981-A-Gchr21-34356981-A-T

Variant summary

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

The ENST00000440403.2(ENSG00000225555):n.855-2094T>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 0.644 in 151,750 control chromosomes in the GnomAD database, including 33,558 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 0.64 (33558 hom., cov: 29)
• Consequence: ENST00000440403.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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
	ENST00000440403.2	n.855-2094T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97646 AN: 151632 Hom.: 33562 Cov.: 29

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.644 AC: 97662 AN: 151750 Hom.: 33558 Cov.: 29 AF XY: 0.650 AC XY: 48183 AN XY: 74150

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.677

Alfa AF: 0.693 Hom.: 17696

Bravo AF: 0.634

Asia WGS AF: 0.741 AC: 2579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.47
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2834467; hg19: chr21-35729280;