rs235925

Positions:

• chr21-27260041-T-C

Variant summary

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

The XR_430359.4(LOC102724355):​n.926+4451A>G 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 0.128 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

LOC102724355 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724355	XR_430359.4	n.926+4451A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0906

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.125

Alfa AF: 0.114 Hom.: 650

Bravo AF: 0.130

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235925; hg19: chr21-28632360;