rs6584475

chr10-102047036-C-G

Variant summary

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

The NM_024541.3(ARMH3):c.-11-6911G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,942 control chromosomes in the GnomAD database, including 23,782 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 0.56 (23782 hom., cov: 32)
• Consequence: ARMH3 NM_024541.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMH3	NM_024541.3	c.-11-6911G>C		intron_variant		ENST00000370033.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMH3	ENST00000370033.9	c.-11-6911G>C		intron_variant		5	NM_024541.3	P1
ARMH3	ENST00000311122.5	c.-11-6911G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84610 AN: 151824 Hom.: 23753 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.557 AC: 84688 AN: 151942 Hom.: 23782 Cov.: 32 AF XY: 0.559 AC XY: 41507 AN XY: 74262

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.583

Alfa AF: 0.570 Hom.: 3043

Bravo AF: 0.555

Asia WGS AF: 0.588 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.59
Dann	Benign	0.56

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: rs6584475; hg19: chr10-103806793;