chr10-101845957-T-C

Variant names:

• chr10-101845957-T-C
• rs1044258
• NM_024541.3:c.*1571A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024541.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMH3	NM_024541.3	MANE Select	c.*1571A>G		3_prime_UTR	Exon 26 of 26	NP_078817.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMH3	ENST00000370033.9	TSL:5 MANE Select	c.*1571A>G		3_prime_UTR	Exon 26 of 26	ENSP00000359050.4
	ARMH3	ENST00000495001.1	TSL:2	n.2106A>G		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.462 AC: 12 AN: 26

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.100 AC: 4166 AN: 41556

American (AMR) AF: 0.290 AC: 4439 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1197 AN: 5168

South Asian (SAS) AF: 0.145 AC: 702 AN: 4826

European-Finnish (FIN) AF: 0.352 AC: 3727 AN: 10588

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23582 AN: 67960

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.317 Hom.: 13657

Bravo AF: 0.250

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.8
DANN	Benign	0.71
PhyloP100		0.22
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: rs1044258; hg19: chr10-103605714;