NM_001001872.4:c.*1051C>T

Variant names:

• chr14-58003685-G-A
• rs2747104
• NM_001001872.4:c.*1051C>T

Variant summary

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

The NM_001001872.4(ARMH4):​c.*1051C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,148 control chromosomes in the GnomAD database, including 4,360 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 0.22 (4360 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: ARMH4 NM_001001872.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 2 publications found

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]

ENSG00000306262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMH4	NM_001001872.4	c.*1051C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000267485.7	NP_001001872.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMH4	ENST00000267485.7	c.*1051C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_001001872.4	ENSP00000267485.7
ARMH4	ENST00000556788.1	n.118+222C>T		intron_variant	Intron 1 of 1	3
ENSG00000306262	ENST00000816531.1	n.160+3807G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33258 AN: 152014 Hom.: 4353 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.125 AC: 2 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 2 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 2 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.219 AC: 33289 AN: 152132 Hom.: 4360 Cov.: 32 AF XY: 0.223 AC XY: 16561 AN XY: 74368

African (AFR) AF: 0.0953 AC: 3956 AN: 41520

American (AMR) AF: 0.290 AC: 4435 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2904 AN: 5166

South Asian (SAS) AF: 0.285 AC: 1370 AN: 4810

European-Finnish (FIN) AF: 0.218 AC: 2308 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16710 AN: 67984

Other (OTH) AF: 0.233 AC: 493 AN: 2112

Alfa AF: 0.236 Hom.: 5491

Bravo AF: 0.221

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		0.091
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: rs2747104; hg19: chr14-58470403;