rs235936

Variant names:

• chr21-27244206-G-A
• rs235936
• XR_430359.4:n.926+20286C>T

Variant summary

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

The XR_430359.4(LOC102724355):​n.926+20286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,934 control chromosomes in the GnomAD database, including 27,257 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 0.58 (27257 hom., cov: 32)
• Consequence: LOC102724355 XR_430359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 2 publications found

Genes affected

LOC102724355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	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: 88760 AN: 151816 Hom.: 27218 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.585 AC: 88860 AN: 151934 Hom.: 27257 Cov.: 32 AF XY: 0.583 AC XY: 43304 AN XY: 74234

African (AFR) AF: 0.751 AC: 31117 AN: 41456

American (AMR) AF: 0.579 AC: 8842 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3468

East Asian (EAS) AF: 0.805 AC: 4148 AN: 5152

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4816

European-Finnish (FIN) AF: 0.459 AC: 4842 AN: 10540

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33660 AN: 67926

Other (OTH) AF: 0.582 AC: 1227 AN: 2110

Alfa AF: 0.523 Hom.: 18607

Bravo AF: 0.609

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.68
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs235936; hg19: chr21-28616525;