rs2838063

chr21-41557202-A-C

Variant summary

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

The XR_937738.1(LOC105372809):n.1251+2095T>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 0.192 in 152,182 control chromosomes in the GnomAD database, including 3,085 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 0.19 (3085 hom., cov: 33)
• Consequence: LOC105372809 XR_937738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

Genes affected

LOC105372809 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372809	XR_937738.1	n.1251+2095T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29210 AN: 152064 Hom.: 3088 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.192 AC: 29212 AN: 152182 Hom.: 3085 Cov.: 33 AF XY: 0.191 AC XY: 14192 AN XY: 74406

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.204

Alfa AF: 0.226 Hom.: 4503

Bravo AF: 0.192

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838063; hg19: chr21-42929129;