NM_024541.3:c.-11-6911G>C

Variant names:

• chr10-102047036-C-G
• rs6584475
• NM_024541.3:c.-11-6911G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.97).
• 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 rank	MANE	Protein	UniProt
ARMH3	NM_024541.3	c.-11-6911G>C		intron_variant	Intron 1 of 25	ENST00000370033.9	NP_078817.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMH3	ENST00000370033.9	c.-11-6911G>C		intron_variant	Intron 1 of 25	5	NM_024541.3	ENSP00000359050.4
ARMH3	ENST00000311122.5	c.-11-6911G>C		intron_variant	Intron 1 of 4	1		ENSP00000312408.4

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

African (AFR) AF: 0.481 AC: 19912 AN: 41400

American (AMR) AF: 0.562 AC: 8570 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2191 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3904 AN: 5164

South Asian (SAS) AF: 0.494 AC: 2385 AN: 4826

European-Finnish (FIN) AF: 0.560 AC: 5907 AN: 10544

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39867 AN: 67974

Other (OTH) AF: 0.583 AC: 1231 AN: 2110

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
PhyloP100		-1.5
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: rs6584475; hg19: chr10-103806793;