chr4-99522563-G-A

Variant names:

• chr4-99522563-G-A
• rs13143848
• NM_032149.3:c.191G>A

Variant summary

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

The NM_032149.3(C4orf17):​c.191G>A​(p.Gly64Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,611,828 control chromosomes in the GnomAD database, including 75,761 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.30 (7039 hom., cov: 31)
  • Exomes 𝑓: 0.30 (68722 hom.)
• Consequence: C4orf17 NM_032149.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 24 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 (MetaRNN=8.7961555E-4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 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.191G>A	p.Gly64Glu	missense	Exon 3 of 9	NP_115525.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf17	ENST00000326581.9	TSL:1 MANE Select	c.191G>A	p.Gly64Glu	missense	Exon 3 of 9	ENSP00000322582.4
	C4orf17	ENST00000514652.5	TSL:5	c.191G>A	p.Gly64Glu	missense	Exon 3 of 8	ENSP00000427663.1
	C4orf17	ENST00000477187.1	TSL:2	n.191G>A		non_coding_transcript_exon	Exon 3 of 10	ENSP00000423411.1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45505 AN: 151706 Hom.: 7040 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.341

GnomAD2 exomes AF: 0.290 AC: 72914 AN: 251060 AF XY: 0.302

Gnomad AFR exome AF: 0.335

Gnomad AMR exome AF: 0.198

Gnomad ASJ exome AF: 0.346

Gnomad EAS exome AF: 0.198

Gnomad FIN exome AF: 0.200

Gnomad NFE exome AF: 0.305

Gnomad OTH exome AF: 0.299

GnomAD4 exome AF: 0.303 AC: 441697 AN: 1460004 Hom.: 68722 Cov.: 34 AF XY: 0.308 AC XY: 223552 AN XY: 726450

African (AFR) AF: 0.332 AC: 11103 AN: 33446

American (AMR) AF: 0.208 AC: 9297 AN: 44680

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 9176 AN: 26100

East Asian (EAS) AF: 0.176 AC: 6984 AN: 39686

South Asian (SAS) AF: 0.421 AC: 36311 AN: 86174

European-Finnish (FIN) AF: 0.200 AC: 10687 AN: 53400

Middle Eastern (MID) AF: 0.393 AC: 2265 AN: 5764

European-Non Finnish (NFE) AF: 0.304 AC: 337473 AN: 1110424

Other (OTH) AF: 0.305 AC: 18401 AN: 60330

GnomAD4 genome AF: 0.300 AC: 45519 AN: 151824 Hom.: 7039 Cov.: 31 AF XY: 0.294 AC XY: 21847 AN XY: 74184

African (AFR) AF: 0.330 AC: 13658 AN: 41344

American (AMR) AF: 0.263 AC: 4005 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1032 AN: 5148

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4812

European-Finnish (FIN) AF: 0.199 AC: 2100 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20428 AN: 67926

Other (OTH) AF: 0.340 AC: 717 AN: 2110

Alfa AF: 0.304 Hom.: 35251

Bravo AF: 0.301

TwinsUK AF: 0.302 AC: 1118

ALSPAC AF: 0.317 AC: 1222

ESP6500AA AF: 0.336 AC: 1479

ESP6500EA AF: 0.308 AC: 2649

ExAC AF: 0.297 AC: 36117

Asia WGS AF: 0.334 AC: 1162 AN: 3478

EpiCase AF: 0.319

EpiControl AF: 0.328

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.76	T
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.5
DANN	Benign	0.48
DEOGEN2	Benign	0.0040	T
Eigen	Benign	-0.82
Eigen_PC	Benign	-0.89
FATHMM_MKL	Benign	0.016	N
LIST_S2	Benign	0.38	T
MetaRNN	Benign	0.00088	T
MetaSVM	Benign	-0.93	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		0.11
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.040
Sift	Benign	0.38	T
Sift4G	Benign	0.18	T
Polyphen		0.23	B
Vest4		0.071
MPC		0.15
ClinPred		0.0021	T
GERP RS		1.2
Varity_R		0.038
gMVP		0.21
Mutation Taster		=99/1	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: rs13143848; hg19: chr4-100443720; COSMIC: COSV58511611;