14-58106465-C-G

Position:

• chr14-58106465-C-G

Variant summary

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

The NM_001001872.4(ARMH4):​c.1832-9484G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,090 control chromosomes in the GnomAD database, including 17,877 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 0.47 (17877 hom., cov: 33)
• Consequence: ARMH4 NM_001001872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

Genes affected

ARMH4 (HGNC:19846): (armadillo like helical domain containing 4) Predicted to be integral component of membrane. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMH4	NM_001001872.4	c.1832-9484G>C		intron_variant		ENST00000267485.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMH4	ENST00000267485.7	c.1832-9484G>C		intron_variant		1	NM_001001872.4	P1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71639 AN: 151972 Hom.: 17889 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.471 AC: 71632 AN: 152090 Hom.: 17877 Cov.: 33 AF XY: 0.466 AC XY: 34623 AN XY: 74346

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.507

Alfa AF: 0.503 Hom.: 2439

Bravo AF: 0.466

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.68

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: rs10134110; hg19: chr14-58573183;