rs6895327

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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: Benign. The variant received -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.

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>T		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>T		intron	N/A	ENSP00000303490.2	Q96MH7
	C5orf34	ENST00000951952.1		c.1153-3202C>T		intron	N/A	ENSP00000622011.1
	C5orf34	ENST00000503655.2	TSL:5	n.354-3202C>T		intron	N/A	ENSP00000426724.2	H0YAD0

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

African (AFR) AF: 0.589 AC: 24398 AN: 41454

American (AMR) AF: 0.411 AC: 6282 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.0907 AC: 470 AN: 5182

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4814

European-Finnish (FIN) AF: 0.436 AC: 4610 AN: 10564

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33037 AN: 67970

Other (OTH) AF: 0.511 AC: 1080 AN: 2112

Alfa AF: 0.477 Hom.: 8830

Bravo AF: 0.491

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.046
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: rs6895327; hg19: chr5-43497905;