21-33990440-A-T

Position:

• chr21-33990440-A-T

Variant summary

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

The XR_937681.3(LOC105372790):​n.1201+5911A>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 0.564 in 151,284 control chromosomes in the GnomAD database, including 24,857 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 0.56 (24857 hom., cov: 29)
• Consequence: LOC105372790 XR_937681.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

Genes affected

LOC105372790 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372790	XR_937681.3	n.1201+5911A>T		intron_variant, non_coding_transcript_variant
LOC105372790	XR_937680.3	n.1201+5911A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85265 AN: 151168 Hom.: 24824 Cov.: 29

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.564 AC: 85354 AN: 151284 Hom.: 24857 Cov.: 29 AF XY: 0.563 AC XY: 41594 AN XY: 73866

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.585

Alfa AF: 0.527 Hom.: 2665

Bravo AF: 0.584

Asia WGS AF: 0.684 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2834327; hg19: chr21-35362741;