Variant rs2304367 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378107.1(R3HDM1):c.2563+58C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.992 in 1,586,016 control chromosomes in the GnomAD database, including 780,208 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 0.97 ( 71883 hom., cov: 31)

Exomes 𝑓: 0.99 ( 708325 hom. )

Consequence

R3HDM1
NM_001378107.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.289

Variant links:

Genes affected

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

R3HDM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
R3HDM1	NM_001378107.1 linkuse as main transcript	c.2563+58C>A		intron_variant		ENST00000683871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
R3HDM1	ENST00000683871.1 linkuse as main transcript	c.2563+58C>A		intron_variant			NM_001378107.1	A1

Frequencies

GnomAD3 genomes

AF:

0.971

AC:

147720

AN:

152184

Hom.:

71832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.907

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.985

Gnomad ASJ

AF:

0.985

Gnomad EAS

AF:

0.983

Gnomad SAS

AF:

0.966

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.979

GnomAD4 exome

AF:

0.994

AC:

1424908

AN:

1433714

Hom.:

708325

AF XY:

0.993

AC XY:

708128

AN XY:

712916

show subpopulations

Gnomad4 AFR exome

AF:

0.899

Gnomad4 AMR exome

AF:

0.994

Gnomad4 ASJ exome

AF:

0.979

Gnomad4 EAS exome

AF:

0.975

Gnomad4 SAS exome

AF:

0.969

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.989

GnomAD4 genome

AF:

0.971

AC:

147830

AN:

152302

Hom.:

71883

Cov.:

AF XY:

0.970

AC XY:

72246

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.907

Gnomad4 AMR

AF:

0.985

Gnomad4 ASJ

AF:

0.985

Gnomad4 EAS

AF:

0.983

Gnomad4 SAS

AF:

0.966

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.980

Alfa

AF:

0.976

Hom.:

11072

Bravo

AF:

0.967

Asia WGS

AF:

0.962

AC:

3347

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.7

DANN

Benign

0.65

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over