10-59360724-C-T

Variant names:

• chr10-59360724-C-T
• rs6481464
• NM_198215.4:c.62+1675G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198215.4(FAM13C):​c.62+1675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,710 control chromosomes in the GnomAD database, including 6,060 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 0.28 (6060 hom., cov: 30)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.990
• Publications: 1 publications found

Genes affected

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

ENSG00000287969 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.62+1675G>A		intron_variant	Intron 1 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.62+1675G>A		intron_variant	Intron 1 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41760 AN: 151594 Hom.: 6049 Cov.: 30

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.276 AC: 41809 AN: 151710 Hom.: 6060 Cov.: 30 AF XY: 0.281 AC XY: 20852 AN XY: 74164

African (AFR) AF: 0.311 AC: 12868 AN: 41344

American (AMR) AF: 0.370 AC: 5644 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3460

East Asian (EAS) AF: 0.409 AC: 2106 AN: 5148

South Asian (SAS) AF: 0.309 AC: 1483 AN: 4794

European-Finnish (FIN) AF: 0.267 AC: 2807 AN: 10506

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 14998 AN: 67898

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.236 Hom.: 2732

Bravo AF: 0.286

Asia WGS AF: 0.351 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.69
PhyloP100		0.99
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: rs6481464; hg19: chr10-61120484;