rs3829908

Positions:

• chr10-44968652-A-G
• chr10-44968652-A-T

Variant summary

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

The NM_032023.4(RASSF4):​c.-38-1513A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,066 control chromosomes in the GnomAD database, including 31,986 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 0.64 (31986 hom., cov: 33)
• Consequence: RASSF4 NM_032023.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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]

LOC105378281 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASSF4	NM_032023.4	c.-38-1513A>G		intron_variant		ENST00000340258.10
LOC105378281	XR_945915.4	n.2735T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASSF4	ENST00000340258.10	c.-38-1513A>G		intron_variant		1	NM_032023.4	P1
RASSF4	ENST00000489171.5	n.461-1513A>G		intron_variant, non_coding_transcript_variant		1
RASSF4	ENST00000427758.5	c.-38-1513A>G		intron_variant		3
RASSF4	ENST00000483709.6	c.-38-1513A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97471 AN: 151948 Hom.: 31965 Cov.: 33

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.641 AC: 97535 AN: 152066 Hom.: 31986 Cov.: 33 AF XY: 0.642 AC XY: 47745 AN XY: 74346

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.629

Alfa AF: 0.681 Hom.: 10139

Bravo AF: 0.630

Asia WGS AF: 0.489 AC: 1700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.96

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: rs3829908; hg19: chr10-45464100;