rs388972

Positions:

• chr10-59318349-G-A
• chr10-59318349-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.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

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 (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM13C	NM_198215.4	c.443+5639C>T		intron_variant		ENST00000618804.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM13C	ENST00000618804.5	c.443+5639C>T		intron_variant		1	NM_198215.4	A1

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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.384

Alfa AF: 0.379 Hom.: 2039

Bravo AF: 0.411

Asia WGS AF: 0.439 AC: 1524 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	1.4
DANN	Benign	0.75

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: rs388972; hg19: chr10-61078109;