rs10519919

Variant names:

• chr5-127065120-T-C
• rs10519919
• NM_001164478.2:c.-7-6118A>G

Variant summary

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

The NM_001164478.2(C5orf63):​c.-7-6118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,306 control chromosomes in the GnomAD database, including 77 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 0.020 (77 hom., cov: 32)
• Consequence: C5orf63 NM_001164478.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792
• Publications: 0 publications found

Genes affected

C5orf63 (HGNC:40051): (chromosome 5 open reading frame 63)

ENSG00000298097 (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 (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164478.2. 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
	C5orf63	NM_001164478.2	MANE Select	c.-7-6118A>G		intron	N/A	NP_001157950.1	A6NC05-2
	C5orf63	NM_001164479.2		c.-7-6118A>G		intron	N/A	NP_001157951.1	A6NC05-1
	C5orf63	NM_001388304.1		c.-7-6118A>G		intron	N/A	NP_001375233.1	A0A8C8V477

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf63	ENST00000296662.10	TSL:5 MANE Select	c.-7-6118A>G		intron	N/A	ENSP00000453964.1	A6NC05-2
	C5orf63	ENST00000535381.6	TSL:3	c.-7-6118A>G		intron	N/A	ENSP00000454153.1	A6NC05-1
	C5orf63	ENST00000607731.5	TSL:5	c.-7-6118A>G		intron	N/A	ENSP00000476160.1	U3KQR4

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3122 AN: 152188 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0297

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0205 AC: 3116 AN: 152306 Hom.: 77 Cov.: 32 AF XY: 0.0232 AC XY: 1729 AN XY: 74484

African (AFR) AF: 0.0118 AC: 489 AN: 41578

American (AMR) AF: 0.0127 AC: 195 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.0912 AC: 472 AN: 5178

South Asian (SAS) AF: 0.117 AC: 562 AN: 4818

European-Finnish (FIN) AF: 0.0297 AC: 315 AN: 10622

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 868 AN: 68022

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.0133 Hom.: 6

Bravo AF: 0.0170

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		0.79
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10519919;

hg19: chr5-126400812;