rs34014631

Variant names:

• chr10-101938948-G-A
• rs34014631
• NM_024541.3:c.1781+915C>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.1781+915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 152,008 control chromosomes in the GnomAD database, including 253 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 0.055 (253 hom., cov: 32)
• Consequence: ARMH3 NM_024541.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 15 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMH3	NM_024541.3	c.1781+915C>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.1781+915C>T		intron_variant	Intron 23 of 25	5	NM_024541.3	ENSP00000359050.4

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8410 AN: 151890 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0554 AC: 8425 AN: 152008 Hom.: 253 Cov.: 32 AF XY: 0.0560 AC XY: 4157 AN XY: 74294

African (AFR) AF: 0.0585 AC: 2423 AN: 41426

American (AMR) AF: 0.0478 AC: 730 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5168

South Asian (SAS) AF: 0.0524 AC: 252 AN: 4812

European-Finnish (FIN) AF: 0.0563 AC: 595 AN: 10572

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3945 AN: 67966

Other (OTH) AF: 0.0507 AC: 107 AN: 2110

Alfa AF: 0.0513 Hom.: 355

Bravo AF: 0.0539

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.054
DANN	Benign	0.25
PhyloP100		-0.67
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: rs34014631; hg19: chr10-103698705;