4-99520729-A-G

Position:

• chr4-99520729-A-G

Variant summary

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

The NM_032149.3(C4orf17):​c.128-1771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,114 control chromosomes in the GnomAD database, including 28,525 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 0.60 (28525 hom., cov: 32)
• Consequence: C4orf17 NM_032149.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

C4orf17 (HGNC:25274): (chromosome 4 open reading frame 17)

C4orf17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C4orf17	NM_032149.3	c.128-1771A>G		intron_variant		ENST00000326581.9	NP_115525.2
C4orf17	XM_011532315.3	c.128-1771A>G		intron_variant			XP_011530617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C4orf17	ENST00000326581.9	c.128-1771A>G		intron_variant		1	NM_032149.3	ENSP00000322582.4
C4orf17	ENST00000514652.5	c.128-1771A>G		intron_variant		5		ENSP00000427663.1
C4orf17	ENST00000477187.1	n.128-1771A>G		intron_variant		2		ENSP00000423411.1
C4orf17	ENST00000503257.1	n.124+1364A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91608 AN: 151996 Hom.: 28485 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.603 AC: 91698 AN: 152114 Hom.: 28525 Cov.: 32 AF XY: 0.609 AC XY: 45289 AN XY: 74378

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.544

Alfa AF: 0.625 Hom.: 46507

Bravo AF: 0.597

Asia WGS AF: 0.578 AC: 2004 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.46

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: rs1354368; hg19: chr4-100441886;