10-18661626-T-C

Variant names:

• chr10-18661626-T-C
• rs10829156
• NM_178815.5:c.46+1943T>C

Variant summary

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

The NM_178815.5(ARL5B):​c.46+1943T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,164 control chromosomes in the GnomAD database, including 47,307 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 0.79 (47307 hom., cov: 33)
• Consequence: ARL5B NM_178815.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 23 publications found

Genes affected

ARL5B (HGNC:23052): (ADP ribosylation factor like GTPase 5B) ARL5B (ARL8) belongs to a family of proteins that are structurally similar to ADP-ribosylation factors (ARFs; see MIM 103180). ARLs and ARFs are part of the RAS superfamily of regulatory GTPases.[supplied by OMIM, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL5B	NM_178815.5	c.46+1943T>C		intron_variant	Intron 1 of 5	ENST00000377275.4	NP_848930.1
ARL5B	XM_005252400.2	c.46+1943T>C		intron_variant	Intron 1 of 4		XP_005252457.1
ARL5B	XM_005252401.5	c.-66+1734T>C		intron_variant	Intron 1 of 5		XP_005252458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL5B	ENST00000377275.4	c.46+1943T>C		intron_variant	Intron 1 of 5	1	NM_178815.5	ENSP00000366487.3

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119818 AN: 152046 Hom.: 47294 Cov.: 33

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.788 AC: 119872 AN: 152164 Hom.: 47307 Cov.: 33 AF XY: 0.787 AC XY: 58518 AN XY: 74396

African (AFR) AF: 0.763 AC: 31688 AN: 41504

American (AMR) AF: 0.763 AC: 11677 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2575 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5078 AN: 5186

South Asian (SAS) AF: 0.810 AC: 3902 AN: 4820

European-Finnish (FIN) AF: 0.780 AC: 8254 AN: 10582

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 54083 AN: 67990

Other (OTH) AF: 0.769 AC: 1622 AN: 2110

Alfa AF: 0.789 Hom.: 145385

Bravo AF: 0.783

Asia WGS AF: 0.858 AC: 2980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.53
PhyloP100		0.078
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: rs10829156; hg19: chr10-18950555;