chr10-44980469-C-T

Variant names:

• chr10-44980469-C-T
• rs3758402
• NM_032023.4:c.139-2052C>T

Variant summary

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

The NM_032023.4(RASSF4):​c.139-2052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,060 control chromosomes in the GnomAD database, including 38,223 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 0.71 (38223 hom., cov: 31)
• Consequence: RASSF4 NM_032023.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF4	NM_032023.4	c.139-2052C>T		intron_variant	Intron 3 of 10	ENST00000340258.10	NP_114412.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF4	ENST00000340258.10	c.139-2052C>T		intron_variant	Intron 3 of 10	1	NM_032023.4	ENSP00000339692.4

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107476 AN: 151942 Hom.: 38163 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.708 AC: 107597 AN: 152060 Hom.: 38223 Cov.: 31 AF XY: 0.708 AC XY: 52615 AN XY: 74350

African (AFR) AF: 0.767 AC: 31844 AN: 41492

American (AMR) AF: 0.760 AC: 11618 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3187 AN: 5158

South Asian (SAS) AF: 0.592 AC: 2855 AN: 4824

European-Finnish (FIN) AF: 0.703 AC: 7439 AN: 10576

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46342 AN: 67936

Other (OTH) AF: 0.706 AC: 1489 AN: 2110

Alfa AF: 0.683 Hom.: 55582

Bravo AF: 0.718

Asia WGS AF: 0.648 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.29
DANN	Benign	0.79
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3758402; hg19: chr10-45475917;