10-59318349-G-A

Variant names:

• chr10-59318349-G-A
• rs388972
• NM_198215.4:c.443+5639C>T

Variant summary

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

The NM_198215.4(FAM13C):​c.443+5639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,632 control chromosomes in the GnomAD database, including 12,684 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 0.40 (12684 hom., cov: 31)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198215.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13C	NM_198215.4	MANE Select	c.443+5639C>T		intron	N/A	NP_937858.2	Q8NE31-1
	FAM13C	NM_001347852.2		c.443+5639C>T		intron	N/A	NP_001334781.1	B7Z2K3
	FAM13C	NM_001347849.2		c.443+5639C>T		intron	N/A	NP_001334778.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13C	ENST00000618804.5	TSL:1 MANE Select	c.443+5639C>T		intron	N/A	ENSP00000481854.1	Q8NE31-1
	FAM13C	ENST00000611933.4	TSL:1	c.443+5639C>T		intron	N/A	ENSP00000481830.1	Q8NE31-3
	FAM13C	ENST00000951024.1		c.443+5639C>T		intron	N/A	ENSP00000621083.1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61324 AN: 151514 Hom.: 12677 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.405 AC: 61361 AN: 151632 Hom.: 12684 Cov.: 31 AF XY: 0.404 AC XY: 29942 AN XY: 74090

African (AFR) AF: 0.495 AC: 20478 AN: 41334

American (AMR) AF: 0.373 AC: 5687 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2423 AN: 5138

South Asian (SAS) AF: 0.409 AC: 1962 AN: 4796

European-Finnish (FIN) AF: 0.357 AC: 3741 AN: 10482

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24588 AN: 67882

Other (OTH) AF: 0.384 AC: 804 AN: 2094

Alfa AF: 0.382 Hom.: 3643

Bravo AF: 0.411

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.61
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: rs388972; hg19: chr10-61078109;