10-59262294-G-A

Variant names:

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.510 AC: 7364 AN: 14440

American (AMR) AF: 0.868 AC: 19535 AN: 22512

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 12295 AN: 14912

East Asian (EAS) AF: 0.838 AC: 26597 AN: 31748

South Asian (SAS) AF: 0.722 AC: 34679 AN: 48012

European-Finnish (FIN) AF: 0.887 AC: 27894 AN: 31442

Middle Eastern (MID) AF: 0.810 AC: 1798 AN: 2220

European-Non Finnish (NFE) AF: 0.843 AC: 299163 AN: 354960

Other (OTH) AF: 0.815 AC: 24006 AN: 29438

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

African (AFR) AF: 0.513 AC: 21281 AN: 41450

American (AMR) AF: 0.852 AC: 13027 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2823 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4613 AN: 5156

South Asian (SAS) AF: 0.721 AC: 3469 AN: 4814

European-Finnish (FIN) AF: 0.876 AC: 9274 AN: 10586

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57413 AN: 67966

Other (OTH) AF: 0.786 AC: 1655 AN: 2106

Alfa AF: 0.780 Hom.: 6161

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
PhyloP100		-0.060
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

Publications

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Other links and lift over

dbSNP: rs1459990; hg19: chr10-61022054;