chr10-59299904-A-C

Position:

• chr10-59299904-A-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13C	NM_198215.4	c.507+2897T>G		intron_variant		ENST00000618804.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13C	ENST00000618804.5	c.507+2897T>G		intron_variant		1	NM_198215.4	A1

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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.750

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.076
DANN	Benign	0.51

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: rs284596; hg19: chr10-61059664;