21-27244206-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724355	XR_430359.4	n.926+20286C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;