rs6895327

Positions:

• chr5-43497803-G-A
• chr5-43497803-G-C

Variant summary

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

The NM_198566.4(C5orf34):​c.1153-3202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,060 control chromosomes in the GnomAD database, including 18,843 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 0.49 (18843 hom., cov: 32)
• Consequence: C5orf34 NM_198566.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

C5orf34 (HGNC:24738): (chromosome 5 open reading frame 34)

ENSG00000249492 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf34	NM_198566.4	c.1153-3202C>T		intron_variant		ENST00000306862.7	NP_940968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf34	ENST00000306862.7	c.1153-3202C>T		intron_variant		1	NM_198566.4	ENSP00000303490.2
C5orf34	ENST00000503655.2	n.354-3202C>T		intron_variant		5		ENSP00000426724.2
ENSG00000249492	ENST00000505645.1	n.329+9661G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73943 AN: 151942 Hom.: 18852 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.486 AC: 73946 AN: 152060 Hom.: 18843 Cov.: 32 AF XY: 0.477 AC XY: 35484 AN XY: 74342

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.511

Alfa AF: 0.474 Hom.: 7751

Bravo AF: 0.491

Asia WGS AF: 0.251 AC: 875 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	1.8
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: rs6895327; hg19: chr5-43497905;