rs11888095

Positions:

• chr2-135665214-C-T

Variant summary

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

The NM_001378107.1(R3HDM1):​c.2152+3821C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,136 control chromosomes in the GnomAD database, including 2,818 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 0.17 (2818 hom., cov: 32)
• Consequence: R3HDM1 NM_001378107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

Genes affected

R3HDM1 (HGNC:9757): (R3H domain containing 1) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

LOC124907893 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
R3HDM1	NM_001378107.1	c.2152+3821C>T		intron_variant		ENST00000683871.1	NP_001365036.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
R3HDM1	ENST00000683871.1	c.2152+3821C>T		intron_variant			NM_001378107.1	ENSP00000506980.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25364 AN: 152018 Hom.: 2816 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.167 AC: 25391 AN: 152136 Hom.: 2818 Cov.: 32 AF XY: 0.171 AC XY: 12720 AN XY: 74362

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.168

Alfa AF: 0.116 Hom.: 376

Bravo AF: 0.175

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs11888095; hg19: chr2-136422784;