rs2894409

Variant names:

• chr6-36698750-C-T
• rs2894409
• NM_001257357.2:c.-13+835C>T

Variant summary

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

The NM_001257357.2(RAB44):​c.-13+835C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,770 control chromosomes in the GnomAD database, including 1,080 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 0.12 (1080 hom., cov: 31)
• Consequence: RAB44 NM_001257357.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 4 publications found

Genes affected

RAB44 (HGNC:21068): (RAB44, member RAS oncogene family) Predicted to enable GTP binding activity; GTPase activity; and calcium ion binding activity. Predicted to be located in azurophil granule membrane; plasma membrane; and specific granule membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB44	NM_001257357.2	c.-13+835C>T		intron_variant	Intron 1 of 13	ENST00000612677.6	NP_001244286.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB44	ENST00000612677.6	c.-13+835C>T		intron_variant	Intron 1 of 13	5	NM_001257357.2	ENSP00000481054.1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17465 AN: 151652 Hom.: 1073 Cov.: 31

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0783

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.115 AC: 17487 AN: 151770 Hom.: 1080 Cov.: 31 AF XY: 0.115 AC XY: 8510 AN XY: 74144

African (AFR) AF: 0.0928 AC: 3838 AN: 41366

American (AMR) AF: 0.130 AC: 1986 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0969 AC: 336 AN: 3468

East Asian (EAS) AF: 0.183 AC: 937 AN: 5126

South Asian (SAS) AF: 0.189 AC: 913 AN: 4824

European-Finnish (FIN) AF: 0.0783 AC: 823 AN: 10514

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8269 AN: 67902

Other (OTH) AF: 0.124 AC: 261 AN: 2104

Alfa AF: 0.123 Hom.: 673

Bravo AF: 0.117

Asia WGS AF: 0.160 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.73

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: rs2894409; hg19: chr6-36666527;