NM_006822.3:c.265-19C>T

Variant names:

• chr17-82659676-G-A
• rs2279395
• NM_006822.3:c.265-19C>T

Variant summary

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

The NM_006822.3(RAB40B):​c.265-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,610,226 control chromosomes in the GnomAD database, including 30,039 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 0.17 (2363 hom., cov: 34)
  • Exomes 𝑓: 0.19 (27676 hom.)
• Consequence: RAB40B NM_006822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 10 publications found

Genes affected

RAB40B (HGNC:18284): (RAB40B, member RAS oncogene family) The protein encoded by this gene has similarity to a yeast protein which suggests a role of the gene product in regulating secretory vesicles. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006822.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB40B	NM_006822.3	MANE Select	c.265-19C>T		intron	N/A	NP_006813.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB40B	ENST00000571995.6	TSL:1 MANE Select	c.265-19C>T		intron	N/A	ENSP00000461785.1
	RAB40B	ENST00000574132.5	TSL:2	n.84C>T		non_coding_transcript_exon	Exon 1 of 3
	RAB40B	ENST00000538809.6	TSL:2	c.265-19C>T		intron	N/A	ENSP00000438897.2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25266 AN: 152102 Hom.: 2363 Cov.: 34

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.135

GnomAD2 exomes AF: 0.168 AC: 42144 AN: 250964 AF XY: 0.164

Gnomad AFR exome AF: 0.104

Gnomad AMR exome AF: 0.144

Gnomad ASJ exome AF: 0.0977

Gnomad EAS exome AF: 0.197

Gnomad FIN exome AF: 0.249

Gnomad NFE exome AF: 0.196

Gnomad OTH exome AF: 0.156

GnomAD4 exome AF: 0.189 AC: 275269 AN: 1458006 Hom.: 27676 Cov.: 29 AF XY: 0.185 AC XY: 134146 AN XY: 725514

African (AFR) AF: 0.0969 AC: 3237 AN: 33402

American (AMR) AF: 0.141 AC: 6285 AN: 44668

Ashkenazi Jewish (ASJ) AF: 0.0981 AC: 2561 AN: 26108

East Asian (EAS) AF: 0.229 AC: 9098 AN: 39680

South Asian (SAS) AF: 0.0792 AC: 6822 AN: 86168

European-Finnish (FIN) AF: 0.249 AC: 13308 AN: 53372

Middle Eastern (MID) AF: 0.0763 AC: 440 AN: 5764

European-Non Finnish (NFE) AF: 0.202 AC: 223594 AN: 1108574

Other (OTH) AF: 0.165 AC: 9924 AN: 60270

GnomAD4 genome AF: 0.166 AC: 25265 AN: 152220 Hom.: 2363 Cov.: 34 AF XY: 0.166 AC XY: 12374 AN XY: 74406

African (AFR) AF: 0.107 AC: 4455 AN: 41542

American (AMR) AF: 0.144 AC: 2200 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5186

South Asian (SAS) AF: 0.0816 AC: 394 AN: 4830

European-Finnish (FIN) AF: 0.246 AC: 2605 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13606 AN: 68008

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.166 Hom.: 3947

Bravo AF: 0.154

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.35
PhyloP100		0.57
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		2.0
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: rs2279395; hg19: chr17-80617552; COSMIC: COSV53915398; COSMIC: COSV53915398;