rs1563824

Positions:

• chr10-59272506-G-A
• chr10-59272506-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198215.4(FAM13C):​c.593-2397C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,112 control chromosomes in the GnomAD database, including 5,495 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 0.23 (5495 hom., cov: 32)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.593-2397C>T		intron_variant		ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.593-2397C>T		intron_variant		1	NM_198215.4	ENSP00000481854	A1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35142 AN: 151994 Hom.: 5471 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.232 AC: 35216 AN: 152112 Hom.: 5495 Cov.: 32 AF XY: 0.228 AC XY: 16955 AN XY: 74356

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.198

Alfa AF: 0.190 Hom.: 425

Bravo AF: 0.242

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.66
DANN	Benign	0.21

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

Publications

LitVar

Other links and lift over

dbSNP: rs1563824; hg19: chr10-61032266; COSMIC: COSV53249300; COSMIC: COSV53249300;