6-108861741-C-T

Position:

• chr6-108861741-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.291+3470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,932 control chromosomes in the GnomAD database, including 19,702 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 0.50 (19702 hom., cov: 31)
• Consequence: ARMC2 NM_032131.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC2	NM_032131.6	c.291+3470C>T		intron_variant		ENST00000392644.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC2	ENST00000392644.9	c.291+3470C>T		intron_variant		1	NM_032131.6	P1
ARMC2	ENST00000237512.4	c.291+3470C>T		intron_variant		2
ARMC2	ENST00000368972.7	c.-204-7083C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76477 AN: 151812 Hom.: 19694 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.504 AC: 76531 AN: 151932 Hom.: 19702 Cov.: 31 AF XY: 0.500 AC XY: 37144 AN XY: 74248

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.458

Alfa AF: 0.513 Hom.: 26542

Bravo AF: 0.495

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.72

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: rs1268055; hg19: chr6-109182944;