rs9913559

Variant names:

• chr17-35930065-T-A
• rs9913559
• NM_145654.4:c.276+11A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-35930065-T-A
• chr17-35930065-T-C

Variant summary

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

The NM_145654.4(RDM1):​c.276+11A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,607,872 control chromosomes in the GnomAD database, including 21,430 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 0.16 (1991 hom., cov: 32)
  • Exomes 𝑓: 0.16 (19439 hom.)
• Consequence: RDM1 NM_145654.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 7 publications found

Genes affected

RDM1 (HGNC:19950): (RAD52 motif containing 1) This gene encodes a protein involved in the cellular response to cisplatin, a drug commonly used in chemotherapy. The protein encoded by this gene contains two motifs: a motif found in RAD52, a protein that functions in DNA double-strand breaks and homologous recombination, and an RNA recognition motif (RRM) that is not found in RAD52. The RAD52 motif region in RAD52 is important for protein function and may be involved in DNA binding or oligomerization. Alternatively spliced transcript variants encoding different isoforms have been reported. [provided by RefSeq, Jul 2008]

ENSG00000270240 (HGNC:58767):

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 (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDM1	NM_145654.4	c.276+11A>T		intron_variant	Intron 2 of 6	ENST00000620284.5	NP_663629.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RDM1	ENST00000620284.5	c.276+11A>T		intron_variant	Intron 2 of 6	1	NM_145654.4	ENSP00000483549.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23677 AN: 152172 Hom.: 1986 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.154

GnomAD2 exomes AF: 0.180 AC: 44678 AN: 248888 AF XY: 0.180

Gnomad AFR exome AF: 0.141

Gnomad AMR exome AF: 0.242

Gnomad ASJ exome AF: 0.182

Gnomad EAS exome AF: 0.213

Gnomad FIN exome AF: 0.142

Gnomad NFE exome AF: 0.147

Gnomad OTH exome AF: 0.169

GnomAD4 exome AF: 0.159 AC: 231183 AN: 1455582 Hom.: 19439 Cov.: 31 AF XY: 0.161 AC XY: 116721 AN XY: 723836

African (AFR) AF: 0.141 AC: 4678 AN: 33116

American (AMR) AF: 0.232 AC: 10174 AN: 43876

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 4821 AN: 25948

East Asian (EAS) AF: 0.209 AC: 8266 AN: 39618

South Asian (SAS) AF: 0.260 AC: 22355 AN: 85848

European-Finnish (FIN) AF: 0.143 AC: 7610 AN: 53372

Middle Eastern (MID) AF: 0.173 AC: 891 AN: 5158

European-Non Finnish (NFE) AF: 0.147 AC: 162844 AN: 1108622

Other (OTH) AF: 0.159 AC: 9544 AN: 60024

GnomAD4 genome AF: 0.156 AC: 23713 AN: 152290 Hom.: 1991 Cov.: 32 AF XY: 0.159 AC XY: 11808 AN XY: 74466

African (AFR) AF: 0.137 AC: 5707 AN: 41558

American (AMR) AF: 0.188 AC: 2875 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1124 AN: 5182

South Asian (SAS) AF: 0.277 AC: 1340 AN: 4830

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10612

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10010 AN: 68026

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.152 Hom.: 352

Bravo AF: 0.157

Asia WGS AF: 0.233 AC: 808 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	6.2
DANN	Benign	0.65
PhyloP100		-0.78
PromoterAI		-0.089	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9913559; hg19: chr17-34257069;