XR_430359.4:n.926+4451A>G

Variant names:

• chr21-27260041-T-C
• rs235925
• XR_430359.4:n.926+4451A>G

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+4451A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,126 control chromosomes in the GnomAD database, including 1,527 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 0.13 (1527 hom., cov: 32)
• Consequence: LOC102724355 XR_430359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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: 0.128 AC: 19438 AN: 152008 Hom.: 1521 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.128 AC: 19463 AN: 152126 Hom.: 1527 Cov.: 32 AF XY: 0.127 AC XY: 9448 AN XY: 74372

African (AFR) AF: 0.216 AC: 8967 AN: 41484

American (AMR) AF: 0.0906 AC: 1383 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5184

South Asian (SAS) AF: 0.181 AC: 875 AN: 4830

European-Finnish (FIN) AF: 0.0560 AC: 594 AN: 10598

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6839 AN: 67978

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.124 Hom.: 1454

Bravo AF: 0.130

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.39
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs235925; hg19: chr21-28632360;