rs3740097

chr10-44975830-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032023.4(RASSF4):c.138+3982C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,216 control chromosomes in the GnomAD database, including 21,851 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 0.51 (21851 hom., cov: 26)
• Consequence: RASSF4 NM_032023.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

RASSF4 (HGNC:20793): (Ras association domain family member 4) The function of this gene has not yet been determined but may involve a role in tumor suppression. Alternative splicing of this gene results in several transcript variants; however, most of the variants have not been fully described. [provided by RefSeq, Jul 2008]

DEPP1 (HGNC:23355): (DEPP autophagy regulator 1) The expression of this gene is induced by fasting as well as by progesterone. The protein encoded by this gene contains a t-synaptosome-associated protein receptor (SNARE) coiled-coil homology domain and a peroxisomal targeting signal. Production of the encoded protein leads to phosphorylation and activation of the transcription factor ELK1. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASSF4	NM_032023.4	c.138+3982C>G		intron_variant		ENST00000340258.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASSF4	ENST00000340258.10	c.138+3982C>G		intron_variant		1	NM_032023.4	P1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76678 AN: 151094 Hom.: 21838 Cov.: 26

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.507 AC: 76720 AN: 151216 Hom.: 21851 Cov.: 26 AF XY: 0.511 AC XY: 37728 AN XY: 73798

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.545

Alfa AF: 0.565 Hom.: 3244

Bravo AF: 0.490

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.5
Dann	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.97

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

Other links and lift over

dbSNP: rs3740097; hg19: chr10-45471278;