6-108941704-C-T

Position:

• chr6-108941704-C-T

Variant summary

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

The NM_032131.6(ARMC2):​c.1596+4705C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,976 control chromosomes in the GnomAD database, including 25,826 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 0.58 (25826 hom., cov: 32)
• Consequence: ARMC2 NM_032131.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

Genes affected

ARMC2 (HGNC:23045): (armadillo repeat containing 2) Involved in sperm axoneme assembly. Implicated in spermatogenic failure 38. [provided by Alliance of Genome Resources, Apr 2022]

ARMC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMC2	NM_032131.6	c.1596+4705C>T		intron_variant		ENST00000392644.9	NP_115507.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMC2	ENST00000392644.9	c.1596+4705C>T		intron_variant		1	NM_032131.6	ENSP00000376417.4
ARMC2	ENST00000368972.7	c.1101+4705C>T		intron_variant		2		ENSP00000357968.3

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87447 AN: 151858 Hom.: 25802 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.576 AC: 87511 AN: 151976 Hom.: 25826 Cov.: 32 AF XY: 0.579 AC XY: 43024 AN XY: 74260

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.610

Alfa AF: 0.581 Hom.: 3208

Bravo AF: 0.583

Asia WGS AF: 0.718 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.8
DANN	Benign	0.84

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: rs911477; hg19: chr6-109262907;