rs1868751

Positions:

• chr10-59346228-T-C
• chr10-59346228-T-G

Variant summary

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

The NM_198215.4(FAM13C):​c.324+6042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,168 control chromosomes in the GnomAD database, including 2,222 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 0.16 (2222 hom., cov: 33)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13C	NM_198215.4	c.324+6042A>G		intron_variant		ENST00000618804.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13C	ENST00000618804.5	c.324+6042A>G		intron_variant		1	NM_198215.4	A1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24343 AN: 152050 Hom.: 2221 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0963

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.160 AC: 24355 AN: 152168 Hom.: 2222 Cov.: 33 AF XY: 0.159 AC XY: 11817 AN XY: 74410

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.0963

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.164

Alfa AF: 0.0556 Hom.: 50

Bravo AF: 0.166

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.58

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: rs1868751; hg19: chr10-61105988;