chr5-43497803-G-C

Variant names:

• chr5-43497803-G-C
• rs6895327
• NM_198566.4:c.1153-3202C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198566.4(C5orf34):​c.1153-3202C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: C5orf34 NM_198566.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 6 publications found

Genes affected

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

C5orf34-AS1 (HGNC:41061): (C5orf34 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198566.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf34	NM_198566.4	MANE Select	c.1153-3202C>G		intron	N/A	NP_940968.1	Q96MH7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf34	ENST00000306862.7	TSL:1 MANE Select	c.1153-3202C>G		intron	N/A	ENSP00000303490.2	Q96MH7
	C5orf34	ENST00000951952.1		c.1153-3202C>G		intron	N/A	ENSP00000622011.1
	C5orf34	ENST00000503655.2	TSL:5	n.354-3202C>G		intron	N/A	ENSP00000426724.2	H0YAD0

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 8830

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.046

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: rs6895327; hg19: chr5-43497905;