rs1044258

chr10-101845957-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024541.3(ARMH3):c.*1571A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,200 control chromosomes in the GnomAD database, including 6,150 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 0.26 (6146 hom., cov: 32)
  • Exomes 𝑓: 0.46 (4 hom.)
• Consequence: ARMH3 NM_024541.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMH3	NM_024541.3	c.*1571A>G		3_prime_UTR_variant	26/26	ENST00000370033.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMH3	ENST00000370033.9	c.*1571A>G		3_prime_UTR_variant	26/26	5	NM_024541.3	P1
ARMH3	ENST00000495001.1	n.2106A>G		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39719 AN: 152054 Hom.: 6141 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.464 AC: 13 AN: 28 Hom.: 4 Cov.: 0 AF XY: 0.500 AC XY: 13 AN XY: 26

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.261 AC: 39731 AN: 152172 Hom.: 6146 Cov.: 32 AF XY: 0.261 AC XY: 19422 AN XY: 74392

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.273

Alfa AF: 0.324 Hom.: 11207

Bravo AF: 0.250

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.8
Dann	Benign	0.71

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: rs1044258; hg19: chr10-103605714;