rs10485822

Variant names:

• chr20-1265768-C-G
• rs10485822
• ENST00000402452.5:c.1387-886C>G

Variant summary

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

The ENST00000402452.5(RAD21L1):​c.1387-886C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0851 in 152,186 control chromosomes in the GnomAD database, including 606 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 0.085 (606 hom., cov: 32)
• Consequence: RAD21L1 ENST00000402452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 0 publications found

Genes affected

RAD21L1 (HGNC:16271): (RAD21 cohesin complex component like 1) Predicted to enable chromatin binding activity. Predicted to be involved in mitotic sister chromatid cohesion; replication-born double-strand break repair via sister chromatid exchange; and synaptonemal complex assembly. Predicted to act upstream of or within several processes, including double-strand break repair via homologous recombination; homologous chromosome segregation; and seminiferous tubule development. Predicted to be located in lateral element. Predicted to be part of nuclear meiotic cohesin complex and nuclear mitotic cohesin complex. Predicted to be active in synaptonemal complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD21L1	ENST00000402452.5	c.1387-886C>G		intron_variant	Intron 12 of 13	5		ENSP00000385925.1

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12933 AN: 152068 Hom.: 603 Cov.: 32

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0353

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.0998

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

GnomAD4 genome AF: 0.0851 AC: 12945 AN: 152186 Hom.: 606 Cov.: 32 AF XY: 0.0867 AC XY: 6450 AN XY: 74406

African (AFR) AF: 0.0857 AC: 3557 AN: 41508

American (AMR) AF: 0.130 AC: 1983 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3472

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5182

South Asian (SAS) AF: 0.0347 AC: 167 AN: 4818

European-Finnish (FIN) AF: 0.0950 AC: 1006 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0800 AC: 5442 AN: 68002

Other (OTH) AF: 0.0997 AC: 211 AN: 2116

Alfa AF: 0.0835 Hom.: 56

Bravo AF: 0.0865

Asia WGS AF: 0.0400 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.34
PhyloP100		-0.034
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10485822; hg19: chr20-1246412;