6-108951702-C-T

Variant names:

• chr6-108951702-C-T
• rs11153138
• NM_032131.6:c.1597-1331C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032131.6(ARMC2):​c.1597-1331C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,188 control chromosomes in the GnomAD database, including 8,344 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 0.30 (8344 hom., cov: 33)
• Consequence: ARMC2 NM_032131.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• spermatogenic failure 38

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
• non-syndromic male infertility due to sperm motility disorder

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032131.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMC2	NM_032131.6	MANE Select	c.1597-1331C>T		intron	N/A	NP_115507.4
	ARMC2	NM_001286609.2		c.1102-1331C>T		intron	N/A	NP_001273538.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMC2	ENST00000392644.9	TSL:1 MANE Select	c.1597-1331C>T		intron	N/A	ENSP00000376417.4
	ARMC2	ENST00000941042.1		c.1597-1331C>T		intron	N/A	ENSP00000611101.1
	ARMC2	ENST00000896778.1		c.1597-1448C>T		intron	N/A	ENSP00000566837.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45255 AN: 152070 Hom.: 8338 Cov.: 33

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.298 AC: 45278 AN: 152188 Hom.: 8344 Cov.: 33 AF XY: 0.301 AC XY: 22397 AN XY: 74396

African (AFR) AF: 0.0836 AC: 3474 AN: 41560

American (AMR) AF: 0.366 AC: 5601 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3009 AN: 5160

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4681 AN: 10584

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24506 AN: 67978

Other (OTH) AF: 0.307 AC: 648 AN: 2114

Alfa AF: 0.204 Hom.: 506

Bravo AF: 0.288

Asia WGS AF: 0.426 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.69
PhyloP100		-1.1
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: rs11153138; hg19: chr6-109272905; COSMIC: COSV64550510;