rs9323327

Positions:

• chr14-58080057-A-G
• chr14-58080057-A-T

Variant summary

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

The NM_001001872.4(ARMH4):​c.2089+16667T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,744 control chromosomes in the GnomAD database, including 21,356 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 0.53 (21356 hom., cov: 31)
• Consequence: ARMH4 NM_001001872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMH4	NM_001001872.4	c.2089+16667T>C		intron_variant		ENST00000267485.7	NP_001001872.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMH4	ENST00000267485.7	c.2089+16667T>C		intron_variant		1	NM_001001872.4	ENSP00000267485	P1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79825 AN: 151640 Hom.: 21348 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.610

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.526 AC: 79861 AN: 151744 Hom.: 21356 Cov.: 31 AF XY: 0.521 AC XY: 38628 AN XY: 74162

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.542

Alfa AF: 0.554 Hom.: 22473

Bravo AF: 0.527

Asia WGS AF: 0.399 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.68
DANN	Benign	0.40

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: rs9323327; hg19: chr14-58546775;