chr10-101899844-C-A

Variant names:

• chr10-101899844-C-A
• rs1374471
• NM_024541.3:c.1782-10354G>T

Variant summary

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

The NM_024541.3(ARMH3):​c.1782-10354G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,048 control chromosomes in the GnomAD database, including 1,582 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 0.13 (1582 hom., cov: 31)
• Consequence: ARMH3 NM_024541.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 5 publications found

Genes affected

ARMH3 (HGNC:25788): (armadillo like helical domain containing 3) Involved in regulation of Golgi organization. Located in Golgi membrane and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000308403 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMH3	NM_024541.3	c.1782-10354G>T		intron_variant	Intron 23 of 25	ENST00000370033.9	NP_078817.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMH3	ENST00000370033.9	c.1782-10354G>T		intron_variant	Intron 23 of 25	5	NM_024541.3	ENSP00000359050.4
ENSG00000308403	ENST00000833795.1	n.76+2939C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19618 AN: 151930 Hom.: 1581 Cov.: 31

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.129 AC: 19617 AN: 152048 Hom.: 1582 Cov.: 31 AF XY: 0.129 AC XY: 9614 AN XY: 74320

African (AFR) AF: 0.0414 AC: 1719 AN: 41506

American (AMR) AF: 0.164 AC: 2501 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.0660 AC: 341 AN: 5164

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4822

European-Finnish (FIN) AF: 0.173 AC: 1822 AN: 10548

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11837 AN: 67968

Other (OTH) AF: 0.145 AC: 306 AN: 2108

Alfa AF: 0.126 Hom.: 370

Bravo AF: 0.126

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.76
PhyloP100		1.1
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: rs1374471; hg19: chr10-103659601;