21-31793549-G-T

Variant names:

• chr21-31793549-G-T
• rs1537096

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.585 in 152,032 control chromosomes in the GnomAD database, including 26,784 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 0.59 (26784 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.33
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88883 AN: 151914 Hom.: 26766 Cov.: 33

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.585 AC: 88946 AN: 152032 Hom.: 26784 Cov.: 33 AF XY: 0.591 AC XY: 43948 AN XY: 74312

African (AFR) AF: 0.716 AC: 29702 AN: 41462

American (AMR) AF: 0.570 AC: 8708 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3468

East Asian (EAS) AF: 0.772 AC: 3990 AN: 5168

South Asian (SAS) AF: 0.693 AC: 3340 AN: 4820

European-Finnish (FIN) AF: 0.584 AC: 6162 AN: 10556

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33655 AN: 67978

Other (OTH) AF: 0.555 AC: 1169 AN: 2108

Alfa AF: 0.449 Hom.: 1418

Bravo AF: 0.587

Asia WGS AF: 0.752 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	18
DANN	Benign	0.65
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs1537096; hg19: chr21-33165862;