rs313522

Variant names:

• chr2-135673296-T-A
• rs313522
• NM_001378107.1:c.2153-2036T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-135673296-T-A
• chr2-135673296-T-C
• chr2-135673296-T-G

Variant summary

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

The NM_001378107.1(R3HDM1):​c.2153-2036T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,964 control chromosomes in the GnomAD database, including 23,043 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 0.49 (23043 hom., cov: 31)
• Consequence: R3HDM1 NM_001378107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• Publications: 4 publications found

Genes affected

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

ENSG00000308733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
R3HDM1	NM_001378107.1	c.2153-2036T>A		intron_variant	Intron 19 of 26	ENST00000683871.1	NP_001365036.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
R3HDM1	ENST00000683871.1	c.2153-2036T>A		intron_variant	Intron 19 of 26		NM_001378107.1	ENSP00000506980.1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74531 AN: 151846 Hom.: 22984 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.491 AC: 74653 AN: 151964 Hom.: 23043 Cov.: 31 AF XY: 0.502 AC XY: 37298 AN XY: 74270

African (AFR) AF: 0.781 AC: 32354 AN: 41444

American (AMR) AF: 0.595 AC: 9077 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3466

East Asian (EAS) AF: 0.878 AC: 4532 AN: 5164

South Asian (SAS) AF: 0.685 AC: 3305 AN: 4822

European-Finnish (FIN) AF: 0.285 AC: 2999 AN: 10534

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18578 AN: 67954

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.408 Hom.: 1973

Bravo AF: 0.524

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.6
DANN	Benign	0.74
PhyloP100		0.52
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: rs313522; hg19: chr2-136430866;