rs284624

Positions:

• chr10-59274259-G-C

Variant summary

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

The NM_198215.4(FAM13C):​c.593-4150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,058 control chromosomes in the GnomAD database, including 44,433 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 0.75 (44433 hom., cov: 31)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

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

FAM13C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.593-4150C>G		intron_variant		ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.593-4150C>G		intron_variant		1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113289 AN: 151942 Hom.: 44428 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.745 AC: 113321 AN: 152058 Hom.: 44433 Cov.: 31 AF XY: 0.750 AC XY: 55714 AN XY: 74328

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.782

Alfa AF: 0.784 Hom.: 5979

Bravo AF: 0.731

Asia WGS AF: 0.771 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.61

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: rs284624; hg19: chr10-61034019;