NM_198215.4:c.325-4048A>C

Variant names:

• chr10-59328154-T-G
• rs436207
• NM_198215.4:c.325-4048A>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.325-4048A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,082 control chromosomes in the GnomAD database, including 17,525 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 0.46 (17525 hom., cov: 33)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 0 publications found

Genes affected

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

ENSG00000308480 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.325-4048A>C		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.325-4048A>C		intron_variant	Intron 3 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70002 AN: 151962 Hom.: 17492 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.461 AC: 70083 AN: 152082 Hom.: 17525 Cov.: 33 AF XY: 0.458 AC XY: 34049 AN XY: 74360

African (AFR) AF: 0.668 AC: 27704 AN: 41474

American (AMR) AF: 0.402 AC: 6139 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2516 AN: 5162

South Asian (SAS) AF: 0.475 AC: 2290 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3771 AN: 10582

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.369 AC: 25056 AN: 67976

Other (OTH) AF: 0.428 AC: 904 AN: 2114

Alfa AF: 0.361 Hom.: 3853

Bravo AF: 0.472

Asia WGS AF: 0.502 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.75
PhyloP100		-1.6
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: rs436207; hg19: chr10-61087914;