rs7964492

Variant names:

• chr12-57429802-A-C
• rs7964492
• NM_001394031.1:c.-106+918T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-57429802-A-C
• chr12-57429802-A-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.-106+918T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 150,662 control chromosomes in the GnomAD database, including 3,026 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 (3026 hom., cov: 30)
• Consequence: R3HDM2 NM_001394031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDM2	NM_001394031.1	MANE Select	c.-106+918T>G		intron	N/A	NP_001380960.1	B5MCU0
	R3HDM2	NM_001351204.2		c.-106+918T>G		intron	N/A	NP_001338133.1
	R3HDM2	NM_001351207.2		c.-207+918T>G		intron	N/A	NP_001338136.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDM2	ENST00000402412.6	TSL:1 MANE Select	c.-106+918T>G		intron	N/A	ENSP00000385839.1	B5MCU0
	R3HDM2	ENST00000347140.7	TSL:1	c.-106+918T>G		intron	N/A	ENSP00000317903.6	Q9Y2K5-1
	R3HDM2	ENST00000448732.1	TSL:1	c.-36+918T>G		intron	N/A	ENSP00000405777.1	C9J7N6

Frequencies

GnomAD3 genomes AF: 0.185 AC: 27874 AN: 150548 Hom.: 3016 Cov.: 30

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.185 AC: 27895 AN: 150662 Hom.: 3026 Cov.: 30 AF XY: 0.181 AC XY: 13278 AN XY: 73396

African (AFR) AF: 0.0997 AC: 4122 AN: 41360

American (AMR) AF: 0.262 AC: 3778 AN: 14434

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3470

East Asian (EAS) AF: 0.0797 AC: 410 AN: 5146

South Asian (SAS) AF: 0.0916 AC: 441 AN: 4814

European-Finnish (FIN) AF: 0.218 AC: 2242 AN: 10276

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

European-Non Finnish (NFE) AF: 0.231 AC: 15679 AN: 67868

Other (OTH) AF: 0.173 AC: 363 AN: 2094

Alfa AF: 0.118 Hom.: 205

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		-0.31
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7964492;

hg19: chr12-57823585;

COSMIC: COSV59005890;

COSMIC: COSV59005890;