rs1374330

Variant names:

• chr2-135663338-A-C
• rs1374330
• NM_001378107.1:c.2152+1945A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-135663338-A-C
• chr2-135663338-A-G
• chr2-135663338-A-T

Variant summary

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

The NM_001378107.1(R3HDM1):​c.2152+1945A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,138 control chromosomes in the GnomAD database, including 2,579 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 0.15 (2579 hom., cov: 32)
• Consequence: R3HDM1 NM_001378107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
R3HDM1	NM_001378107.1	c.2152+1945A>C		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.2152+1945A>C		intron_variant	Intron 19 of 26		NM_001378107.1	ENSP00000506980.1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22617 AN: 152020 Hom.: 2576 Cov.: 32

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.149 AC: 22633 AN: 152138 Hom.: 2579 Cov.: 32 AF XY: 0.155 AC XY: 11520 AN XY: 74368

African (AFR) AF: 0.0382 AC: 1588 AN: 41544

American (AMR) AF: 0.239 AC: 3651 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2290 AN: 5162

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4814

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10588

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10098 AN: 67968

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.165 Hom.: 1420

Bravo AF: 0.150

Asia WGS AF: 0.335 AC: 1165 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		0.24
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: rs1374330; hg19: chr2-136420908;