NM_032149.3:c.337+818T>C

Variant names:

• chr4-99523527-T-C
• rs13126513
• NM_032149.3:c.337+818T>C

Variant summary

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

The NM_032149.3(C4orf17):​c.337+818T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,098 control chromosomes in the GnomAD database, including 31,873 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 0.62 (31873 hom., cov: 32)
• Consequence: C4orf17 NM_032149.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf17	NM_032149.3	c.337+818T>C		intron_variant	Intron 3 of 8	ENST00000326581.9	NP_115525.2
C4orf17	XM_011532315.3	c.337+818T>C		intron_variant	Intron 3 of 5		XP_011530617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C4orf17	ENST00000326581.9	c.337+818T>C		intron_variant	Intron 3 of 8	1	NM_032149.3	ENSP00000322582.4
C4orf17	ENST00000514652.5	c.337+818T>C		intron_variant	Intron 3 of 7	5		ENSP00000427663.1
C4orf17	ENST00000477187.1	n.337+818T>C		intron_variant	Intron 3 of 9	2		ENSP00000423411.1
C4orf17	ENST00000503257.1	n.334+818T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93521 AN: 151980 Hom.: 31827 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.615 AC: 93610 AN: 152098 Hom.: 31873 Cov.: 32 AF XY: 0.608 AC XY: 45186 AN XY: 74344

African (AFR) AF: 0.899 AC: 37324 AN: 41522

American (AMR) AF: 0.482 AC: 7371 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2520 AN: 3470

East Asian (EAS) AF: 0.772 AC: 4001 AN: 5182

South Asian (SAS) AF: 0.669 AC: 3219 AN: 4810

European-Finnish (FIN) AF: 0.318 AC: 3356 AN: 10556

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33690 AN: 67958

Other (OTH) AF: 0.621 AC: 1311 AN: 2112

Alfa AF: 0.544 Hom.: 88281

Bravo AF: 0.637

Asia WGS AF: 0.671 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.22
DANN	Benign	0.49
PhyloP100		-2.8
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: rs13126513; hg19: chr4-100444684;