6-108951702-C-T

Position:

• chr6-108951702-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.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

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMC2	NM_032131.6	c.1597-1331C>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.1597-1331C>T		intron_variant		1	NM_032131.6	ENSP00000376417.4
ARMC2	ENST00000368972.7	c.1102-1331C>T		intron_variant		2		ENSP00000357968.3

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

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.307

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.69

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: rs11153138; hg19: chr6-109272905; COSMIC: COSV64550510;