10-59362508-T-TTA

Variant names:

• chr10-59362508-T-TTA
• rs3078330
• NM_198215.4:c.-50_-49dupTA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_198215.4(FAM13C):​c.-50_-49dupTA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM13C NM_198215.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 7 publications found

Genes affected

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

ENSG00000287969 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198215.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13C	NM_198215.4	MANE Select	c.-50_-49dupTA		5_prime_UTR	Exon 1 of 14	NP_937858.2
	FAM13C	NM_001347852.2		c.-50_-49dupTA		5_prime_UTR	Exon 1 of 13	NP_001334781.1
	FAM13C	NM_001347849.2		c.-50_-49dupTA		5_prime_UTR	Exon 1 of 13	NP_001334778.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13C	ENST00000618804.5	TSL:1 MANE Select	c.-50_-49dupTA		5_prime_UTR	Exon 1 of 14	ENSP00000481854.1
	FAM13C	ENST00000611933.4	TSL:1	c.-50_-49dupTA		5_prime_UTR	Exon 1 of 12	ENSP00000481830.1
	FAM13C	ENST00000619059.4	TSL:4	n.-50_-49dupTA		non_coding_transcript_exon	Exon 1 of 6	ENSP00000484965.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.999 AC: 233026 AN: 233246 AF XY: 0.999

Gnomad AFR exome AF: 0.987

Gnomad AMR exome AF: 0.999

Gnomad ASJ exome AF: 1.00

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 1.00

Gnomad OTH exome AF: 1.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.492 Hom.: 6760

Asia WGS AF: 0.999 AC: 3475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3078330; hg19: chr10-61122268;