NM_032023.4:c.282-418C>A

Variant names:

• chr10-44983604-C-A
• rs869156
• NM_032023.4:c.282-418C>A

Variant summary

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

The NM_032023.4(RASSF4):​c.282-418C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 193,048 control chromosomes in the GnomAD database, including 30,539 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 0.53 (22897 hom., cov: 33)
  • Exomes 𝑓: 0.60 (7642 hom.)
• Consequence: RASSF4 NM_032023.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF4	NM_032023.4	c.282-418C>A		intron_variant	Intron 4 of 10	ENST00000340258.10	NP_114412.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF4	ENST00000340258.10	c.282-418C>A		intron_variant	Intron 4 of 10	1	NM_032023.4	ENSP00000339692.4

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80252 AN: 151914 Hom.: 22884 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.561

GnomAD4 exome AF: 0.596 AC: 24454 AN: 41016 Hom.: 7642 Cov.: 0 AF XY: 0.585 AC XY: 12659 AN XY: 21656

African (AFR) AF: 0.284 AC: 164 AN: 578

American (AMR) AF: 0.598 AC: 1547 AN: 2588

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 512 AN: 878

East Asian (EAS) AF: 0.318 AC: 390 AN: 1226

South Asian (SAS) AF: 0.498 AC: 2927 AN: 5876

European-Finnish (FIN) AF: 0.654 AC: 1183 AN: 1808

Middle Eastern (MID) AF: 0.536 AC: 90 AN: 168

European-Non Finnish (NFE) AF: 0.635 AC: 16297 AN: 25648

Other (OTH) AF: 0.598 AC: 1344 AN: 2246

GnomAD4 genome AF: 0.528 AC: 80286 AN: 152032 Hom.: 22897 Cov.: 33 AF XY: 0.531 AC XY: 39452 AN XY: 74302

African (AFR) AF: 0.303 AC: 12577 AN: 41472

American (AMR) AF: 0.598 AC: 9132 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1793 AN: 5158

South Asian (SAS) AF: 0.510 AC: 2453 AN: 4808

European-Finnish (FIN) AF: 0.663 AC: 7010 AN: 10574

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43491 AN: 67964

Other (OTH) AF: 0.565 AC: 1188 AN: 2102

Alfa AF: 0.574 Hom.: 4143

Bravo AF: 0.514

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.17
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: rs869156; hg19: chr10-45479052;