chr14-58106465-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001001872.4(ARMH4):​c.1832-9484G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,090 control chromosomes in the GnomAD database, including 17,877 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 0.47 ( 17877 hom., cov: 33)

Consequence

ARMH4
NM_001001872.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.496
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARMH4NM_001001872.4 linkuse as main transcriptc.1832-9484G>C intron_variant ENST00000267485.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARMH4ENST00000267485.7 linkuse as main transcriptc.1832-9484G>C intron_variant 1 NM_001001872.4 P1Q86TY3-1

Frequencies

GnomAD3 genomes
AF:
0.471
AC:
71639
AN:
151972
Hom.:
17889
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.319
Gnomad AMI
AF:
0.749
Gnomad AMR
AF:
0.422
Gnomad ASJ
AF:
0.637
Gnomad EAS
AF:
0.328
Gnomad SAS
AF:
0.448
Gnomad FIN
AF:
0.475
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.573
Gnomad OTH
AF:
0.514
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.471
AC:
71632
AN:
152090
Hom.:
17877
Cov.:
33
AF XY:
0.466
AC XY:
34623
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.318
Gnomad4 AMR
AF:
0.421
Gnomad4 ASJ
AF:
0.637
Gnomad4 EAS
AF:
0.329
Gnomad4 SAS
AF:
0.447
Gnomad4 FIN
AF:
0.475
Gnomad4 NFE
AF:
0.573
Gnomad4 OTH
AF:
0.507
Alfa
AF:
0.503
Hom.:
2439
Bravo
AF:
0.466
Asia WGS
AF:
0.348
AC:
1207
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.5
DANN
Benign
0.68

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10134110; hg19: chr14-58573183; API