rs2141765

Variant names:

• chr12-64526196-C-A
• rs2141765
• ENST00000637125.1:c.170-15385C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-64526196-C-A
• chr12-64526196-C-G
• chr12-64526196-C-T

Variant summary

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

The ENST00000541885.1(ENSG00000256199):​n.307+7136G>T variant causes a intron 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: ENSG00000256199 ENST00000541885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 7 publications found

Genes affected

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]

ENSG00000256199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000541885.1. 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
	LOC105369803	NR_188079.1		n.1153+6752G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RASSF3	ENST00000637125.1	TSL:5	c.170-15385C>A		intron	N/A	ENSP00000490100.1	A0A1B0GUG6
	ENSG00000256199	ENST00000541885.1	TSL:3	n.307+7136G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67244 AN: 151898 Hom.: 16192 Cov.: 32

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.: 32 AF XY: 0.455 AC XY: 33800 AN XY: 74300

African (AFR) AF: 0.281 AC: 11637 AN: 41426

American (AMR) AF: 0.510 AC: 7780 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1663 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4546 AN: 5188

South Asian (SAS) AF: 0.604 AC: 2916 AN: 4824

European-Finnish (FIN) AF: 0.566 AC: 5974 AN: 10550

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31326 AN: 67976

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.461 Hom.: 24177

Bravo AF: 0.432

Asia WGS AF: 0.662 AC: 2299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.16
PhyloP100		-0.34

Splicing

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: rs2141765;

hg19: chr12-64919976;

COSMIC: COSV108275014;