rs284596

Variant names:

• chr10-59299904-A-C
• rs284596
• NM_198215.4:c.507+2897T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-59299904-A-C
• chr10-59299904-A-G
• chr10-59299904-A-T

Variant summary

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

The NM_198215.4(FAM13C):​c.507+2897T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 151,778 control chromosomes in the GnomAD database, including 44,006 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 0.76 (44006 hom., cov: 30)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 0 publications found

Genes affected

FAM13C (HGNC:19371): (family with sequence similarity 13 member C)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198215.4. 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
	FAM13C	NM_198215.4	MANE Select	c.507+2897T>G		intron	N/A	NP_937858.2	Q8NE31-1
	FAM13C	NM_001347852.2		c.507+2897T>G		intron	N/A	NP_001334781.1	B7Z2K3
	FAM13C	NM_001347849.2		c.507+2897T>G		intron	N/A	NP_001334778.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13C	ENST00000618804.5	TSL:1 MANE Select	c.507+2897T>G		intron	N/A	ENSP00000481854.1	Q8NE31-1
	FAM13C	ENST00000611933.4	TSL:1	c.507+2897T>G		intron	N/A	ENSP00000481830.1	Q8NE31-3
	FAM13C	ENST00000951024.1		c.507+2897T>G		intron	N/A	ENSP00000621083.1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115230 AN: 151660 Hom.: 43973 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.760 AC: 115316 AN: 151778 Hom.: 44006 Cov.: 30 AF XY: 0.758 AC XY: 56234 AN XY: 74156

African (AFR) AF: 0.686 AC: 28370 AN: 41362

American (AMR) AF: 0.778 AC: 11837 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3700 AN: 5132

South Asian (SAS) AF: 0.794 AC: 3802 AN: 4788

European-Finnish (FIN) AF: 0.795 AC: 8400 AN: 10566

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53884 AN: 67936

Other (OTH) AF: 0.750 AC: 1580 AN: 2106

Alfa AF: 0.782 Hom.: 9463

Bravo AF: 0.753

Asia WGS AF: 0.782 AC: 2724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.076
DANN	Benign	0.51
PhyloP100		-2.6
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: rs284596; hg19: chr10-61059664;