Variant rs2141765 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000541885.1(ENSG00000256199):n.307+7136G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,016 control chromosomes in the GnomAD database, including 16,193 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 0.44 ( 16193 hom., cov: 32)

Consequence

ENST00000541885.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.339

Variant links:

Genes affected

(HGNC:):

links:

RASSF3 (HGNC:14271): (Ras association domain family member 3) The RAS oncogene (MIM 190020) is mutated in nearly one-third of all human cancers. Members of the RAS superfamily are plasma membrane GTP-binding proteins that modulate intracellular signal transduction pathways. A subfamily of RAS effectors, including RASSF3, share a RAS association (RA) domain.[supplied by OMIM, Jul 2003]

RASSF3 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105369803	XR_002957417.1 linkuse as main transcript	n.534+7136G>T	intron_variant, non_coding_transcript_variant
RASSF3	XM_047428711.1 linkuse as main transcript	c.125-15385C>A	intron_variant
RASSF3	XM_047428712.1 linkuse as main transcript	c.278-15385C>A	intron_variant
LOC105369803	XR_945026.3 linkuse as main transcript	n.793+7136G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000541885.1 linkuse as main transcript	n.307+7136G>T		intron_variant, non_coding_transcript_variant		3
RASSF3	ENST00000637125.1 linkuse as main transcript	c.170-15385C>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67244

AN:

151898

Hom.:

16192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.605

Gnomad FIN

AF:

0.566

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.460

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

GnomAD4 genome

AF:

0.442

AC:

67261

AN:

152016

Hom.:

16193

Cov.:

AF XY:

0.455

AC XY:

33800

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.510

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.876

Gnomad4 SAS

AF:

0.604

Gnomad4 FIN

AF:

0.566

Gnomad4 NFE

AF:

0.461

Gnomad4 OTH

AF:

0.464

Alfa

AF:

0.463

Hom.:

20113

Bravo

AF:

0.432

Asia WGS

AF:

0.662

AC:

2299

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.60

DANN

Benign

0.16

Splicing

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