rs1374471

Positions:

• chr10-101899844-C-A
• chr10-101899844-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ARMH3	NM_024541.3	c.1782-10354G>T		intron_variant		ENST00000370033.9	NP_078817.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMH3	ENST00000370033.9	c.1782-10354G>T		intron_variant		5	NM_024541.3	ENSP00000359050	P1

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

Gnomad4 AFR AF: 0.0414

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0660

Gnomad4 SAS AF: 0.0786

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.145

Alfa AF: 0.128 Hom.: 369

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

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: rs1374471; hg19: chr10-103659601;