chr5-34007604-A-C

Variant names:

• chr5-34007604-A-C
• rs34689
• NM_014324.6:c.247+169T>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_014324.6(AMACR):​c.247+169T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,086 control chromosomes in the GnomAD database, including 6,335 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.25 (6335 hom., cov: 32)
• Consequence: AMACR NM_014324.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.31
• Publications: 4 publications found

Genes affected

AMACR (HGNC:451): (alpha-methylacyl-CoA racemase) This gene encodes a racemase. The encoded enzyme interconverts pristanoyl-CoA and C27-bile acylCoAs between their (R)- and (S)-stereoisomers. The conversion to the (S)-stereoisomers is necessary for degradation of these substrates by peroxisomal beta-oxidation. Encoded proteins from this locus localize to both mitochondria and peroxisomes. Mutations in this gene may be associated with adult-onset sensorimotor neuropathy, pigmentary retinopathy, and adrenomyeloneuropathy due to defects in bile acid synthesis. Alternatively spliced transcript variants have been described. Read-through transcription also exists between this gene and the upstream neighboring C1QTNF3 (C1q and tumor necrosis factor related protein 3) gene. [provided by RefSeq, Mar 2011]

ENSG00000289791 (HGNC:):

C1QTNF3-AMACR (HGNC:49198): (C1QTNF3-AMACR readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C1q and tumor necrosis factor related protein 3 (C1QTNF3) and alpha-methylacyl-CoA racemase (AMACR) genes on chromosome 5. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus not likely to produce a protein product. [provided by RefSeq, Mar 2011]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 5-34007604-A-C is Benign according to our data. Variant chr5-34007604-A-C is described in ClinVar as Benign. ClinVar VariationId is 1268751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014324.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMACR	NM_014324.6	MANE Select	c.247+169T>G		intron	N/A	NP_055139.4
	AMACR	NM_001167595.2		c.247+169T>G		intron	N/A	NP_001161067.1
	AMACR	NM_203382.3		c.247+169T>G		intron	N/A	NP_976316.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMACR	ENST00000335606.11	TSL:1 MANE Select	c.247+169T>G		intron	N/A	ENSP00000334424.6
	AMACR	ENST00000382085.7	TSL:1	c.247+169T>G		intron	N/A	ENSP00000371517.3
	ENSG00000289791	ENST00000426255.6	TSL:2	c.247+169T>G		intron	N/A	ENSP00000476965.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38686 AN: 151968 Hom.: 6305 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.255 AC: 38752 AN: 152086 Hom.: 6335 Cov.: 32 AF XY: 0.252 AC XY: 18757 AN XY: 74354

African (AFR) AF: 0.471 AC: 19527 AN: 41426

American (AMR) AF: 0.158 AC: 2410 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.164 AC: 845 AN: 5168

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4816

European-Finnish (FIN) AF: 0.171 AC: 1813 AN: 10594

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11642 AN: 68002

Other (OTH) AF: 0.237 AC: 500 AN: 2114

Alfa AF: 0.194 Hom.: 2110

Bravo AF: 0.265

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Sep 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-1.3
PromoterAI		0.048	Neutral
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: rs34689; hg19: chr5-34007709;