10-59256873-T-C

Variant names:

• chr10-59256873-T-C
• rs2452503
• NM_198215.4:c.1237-2430A>G

Variant summary

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

The NM_198215.4(FAM13C):​c.1237-2430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,140 control chromosomes in the GnomAD database, including 45,386 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 (45386 hom., cov: 32)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

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=-0.97).
• 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 rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.1237-2430A>G		intron_variant	Intron 10 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.1237-2430A>G		intron_variant	Intron 10 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115066 AN: 152022 Hom.: 45382 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.757 AC: 115098 AN: 152140 Hom.: 45386 Cov.: 32 AF XY: 0.761 AC XY: 56584 AN XY: 74362

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.787

Alfa AF: 0.721 Hom.: 2788

Bravo AF: 0.745

Asia WGS AF: 0.772 AC: 2682 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	6.4
DANN	Benign	0.86

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: rs2452503; hg19: chr10-61016633;