chr10-59301747-A-G

Position:

• chr10-59301747-A-G

Variant summary

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

The NM_198215.4(FAM13C):​c.507+1054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,116 control chromosomes in the GnomAD database, including 26,663 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 0.58 (26663 hom., cov: 33)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.507+1054T>C		intron_variant		ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.507+1054T>C		intron_variant		1	NM_198215.4	ENSP00000481854	A1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88101 AN: 151998 Hom.: 26639 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.580 AC: 88165 AN: 152116 Hom.: 26663 Cov.: 33 AF XY: 0.581 AC XY: 43220 AN XY: 74366

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.588

Alfa AF: 0.600 Hom.: 5167

Bravo AF: 0.571

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs373304; hg19: chr10-61061507;