rs1459990

Variant names:

• chr10-59262294-G-A
• rs1459990
• NM_198215.4:c.1236+140C>T

Variant summary

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

The NM_198215.4(FAM13C):​c.1236+140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 701,722 control chromosomes in the GnomAD database, including 233,490 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 0.75 (45078 hom., cov: 32)
  • Exomes 𝑓: 0.82 (188412 hom.)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.1236+140C>T		intron_variant	Intron 10 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.1236+140C>T		intron_variant	Intron 10 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114556 AN: 151920 Hom.: 45067 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.786

GnomAD4 exome AF: 0.825 AC: 453331 AN: 549684 Hom.: 188412 AF XY: 0.821 AC XY: 235974 AN XY: 287574

Gnomad4 AFR exome AF: 0.510

Gnomad4 AMR exome AF: 0.868

Gnomad4 ASJ exome AF: 0.825

Gnomad4 EAS exome AF: 0.838

Gnomad4 SAS exome AF: 0.722

Gnomad4 FIN exome AF: 0.887

Gnomad4 NFE exome AF: 0.843

Gnomad4 OTH exome AF: 0.815

GnomAD4 genome AF: 0.754 AC: 114603 AN: 152038 Hom.: 45078 Cov.: 32 AF XY: 0.757 AC XY: 56295 AN XY: 74332

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.786

Alfa AF: 0.791 Hom.: 6046

Bravo AF: 0.744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.26

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: rs1459990; hg19: chr10-61022054;