10-59249936-C-G

Variant names:

• chr10-59249936-C-G
• rs1380555
• NM_198215.4:c.1634+1639G>C

Variant summary

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

The NM_198215.4(FAM13C):​c.1634+1639G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,084 control chromosomes in the GnomAD database, including 44,584 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 (44584 hom., cov: 33)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 1 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=-0.75).
• 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.1634+1639G>C		intron_variant	Intron 13 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.1634+1639G>C		intron_variant	Intron 13 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113521 AN: 151966 Hom.: 44578 Cov.: 33

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.747 AC: 113558 AN: 152084 Hom.: 44584 Cov.: 33 AF XY: 0.751 AC XY: 55870 AN XY: 74362

African (AFR) AF: 0.483 AC: 20018 AN: 41426

American (AMR) AF: 0.850 AC: 12993 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2819 AN: 3468

East Asian (EAS) AF: 0.896 AC: 4628 AN: 5166

South Asian (SAS) AF: 0.719 AC: 3466 AN: 4820

European-Finnish (FIN) AF: 0.895 AC: 9483 AN: 10596

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57458 AN: 68000

Other (OTH) AF: 0.781 AC: 1646 AN: 2108

Alfa AF: 0.785 Hom.: 5999

Bravo AF: 0.733

Asia WGS AF: 0.770 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.19
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: rs1380555; hg19: chr10-61009696;