4-99520729-A-G

Variant names:

• chr4-99520729-A-G
• rs1354368
• NM_032149.3:c.128-1771A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032149.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf17	NM_032149.3	MANE Select	c.128-1771A>G		intron	N/A	NP_115525.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf17	ENST00000326581.9	TSL:1 MANE Select	c.128-1771A>G		intron	N/A	ENSP00000322582.4
	C4orf17	ENST00000514652.5	TSL:5	c.128-1771A>G		intron	N/A	ENSP00000427663.1
	C4orf17	ENST00000477187.1	TSL:2	n.128-1771A>G		intron	N/A	ENSP00000423411.1

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

African (AFR) AF: 0.482 AC: 19980 AN: 41478

American (AMR) AF: 0.658 AC: 10061 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3466

East Asian (EAS) AF: 0.792 AC: 4100 AN: 5176

South Asian (SAS) AF: 0.453 AC: 2186 AN: 4826

European-Finnish (FIN) AF: 0.750 AC: 7936 AN: 10580

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43993 AN: 67986

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.624 Hom.: 72248

Bravo AF: 0.597

Asia WGS AF: 0.578 AC: 2004 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.46
PhyloP100		-1.2
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: rs1354368; hg19: chr4-100441886;