rs737820

chr22-23161683-A-G

Variant summary

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

The NM_004914.5(RAB36):c.*119A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 868,854 control chromosomes in the GnomAD database, including 105,981 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 (20102 hom., cov: 33)
  • Exomes 𝑓: 0.49 (85879 hom.)
• Consequence: RAB36 NM_004914.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

RAB36 (HGNC:9775): (RAB36, member RAS oncogene family) Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in protein transport. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

RSPH14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB36	NM_004914.5	c.*119A>G		3_prime_UTR_variant	11/11	ENST00000263116.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB36	ENST00000263116.8	c.*119A>G		3_prime_UTR_variant	11/11	1	NM_004914.5	P1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77759 AN: 151924 Hom.: 20075 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.485 AC: 347785 AN: 716812 Hom.: 85879 Cov.: 9 AF XY: 0.491 AC XY: 179442 AN XY: 365650

Gnomad4 AFR exome AF: 0.512

Gnomad4 AMR exome AF: 0.470

Gnomad4 ASJ exome AF: 0.480

Gnomad4 EAS exome AF: 0.626

Gnomad4 SAS exome AF: 0.592

Gnomad4 FIN exome AF: 0.426

Gnomad4 NFE exome AF: 0.468

Gnomad4 OTH exome AF: 0.493

GnomAD4 genome AF: 0.512 AC: 77838 AN: 152042 Hom.: 20102 Cov.: 33 AF XY: 0.514 AC XY: 38174 AN XY: 74312

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.511

Alfa AF: 0.500 Hom.: 5845

Bravo AF: 0.512

Asia WGS AF: 0.606 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.4
Dann	Benign	0.55

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: rs737820; hg19: chr22-23503870; COSMIC: COSV54076674; COSMIC: COSV54076674;