10-59338100-T-C

Variant names:

• chr10-59338100-T-C
• rs1413835
• NM_198215.4:c.325-13994A>G

Variant summary

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

The NM_198215.4(FAM13C):​c.325-13994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,870 control chromosomes in the GnomAD database, including 38,198 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 0.70 (38198 hom., cov: 32)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 0 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.325-13994A>G		intron_variant	Intron 3 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.325-13994A>G		intron_variant	Intron 3 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106797 AN: 151752 Hom.: 38182 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.704 AC: 106856 AN: 151870 Hom.: 38198 Cov.: 32 AF XY: 0.704 AC XY: 52250 AN XY: 74208

African (AFR) AF: 0.576 AC: 23849 AN: 41394

American (AMR) AF: 0.718 AC: 10963 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2730 AN: 3468

East Asian (EAS) AF: 0.834 AC: 4311 AN: 5172

South Asian (SAS) AF: 0.724 AC: 3482 AN: 4812

European-Finnish (FIN) AF: 0.741 AC: 7798 AN: 10520

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51251 AN: 67922

Other (OTH) AF: 0.732 AC: 1541 AN: 2106

Alfa AF: 0.711 Hom.: 4785

Bravo AF: 0.698

Asia WGS AF: 0.715 AC: 2487 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	2.0
DANN	Benign	0.52
PhyloP100		-0.011
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: rs1413835; hg19: chr10-61097860;