rs11172147

Variant names:

• chr12-57302894-G-A
• rs11172147
• NM_001394031.1:c.207+282C>T

Variant summary

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

The NM_001394031.1(R3HDM2):​c.207+282C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,040 control chromosomes in the GnomAD database, including 3,111 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 (3111 hom., cov: 31)
• Consequence: R3HDM2 NM_001394031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 11 publications found

Genes affected

R3HDM2 (HGNC:29167): (R3H domain containing 2) Enables RNA binding activity. Predicted to be located in nucleus. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394031.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDM2	NM_001394031.1	MANE Select	c.207+282C>T		intron	N/A	NP_001380960.1
	R3HDM2	NM_001351204.2		c.207+282C>T		intron	N/A	NP_001338133.1
	R3HDM2	NM_001351205.2		c.207+282C>T		intron	N/A	NP_001338134.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDM2	ENST00000402412.6	TSL:1 MANE Select	c.207+282C>T		intron	N/A	ENSP00000385839.1
	R3HDM2	ENST00000347140.7	TSL:1	c.207+282C>T		intron	N/A	ENSP00000317903.6
	R3HDM2	ENST00000403821.6	TSL:5	c.207+282C>T		intron	N/A	ENSP00000385169.2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28327 AN: 151924 Hom.: 3101 Cov.: 31

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0984

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.186 AC: 28348 AN: 152040 Hom.: 3111 Cov.: 31 AF XY: 0.184 AC XY: 13684 AN XY: 74324

African (AFR) AF: 0.0949 AC: 3938 AN: 41478

American (AMR) AF: 0.280 AC: 4280 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3468

East Asian (EAS) AF: 0.0980 AC: 508 AN: 5182

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4824

European-Finnish (FIN) AF: 0.229 AC: 2415 AN: 10536

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15628 AN: 67962

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.215 Hom.: 5914

Bravo AF: 0.194

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.66
PhyloP100		-0.038
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: rs11172147; hg19: chr12-57696677;