19-3543480-GCCCCCC-GCCCCCCCCCCCC

Position:

• chr19-3543480-GCCCCCC-GCCCCCCCCCCCC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001135580.2(TEKTIP1):​c.322+13_322+18dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00041 (1 hom., cov: 0)
  • Exomes 𝑓: 0.000039 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEKTIP1 NM_001135580.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

Genes affected

TEKTIP1 (HGNC:34496): (tektin bundle interacting protein 1)

MFSD12 (HGNC:28299): (major facilitator superfamily domain containing 12) Enables cysteine transmembrane transporter activity. Involved in cysteine transmembrane transport; pigment metabolic process involved in pigmentation; and regulation of melanin biosynthetic process. Located in lysosome and melanosome. Part of late endosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKTIP1	NM_001135580.2	c.322+13_322+18dup		splice_region_variant, intron_variant		ENST00000329493.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKTIP1	ENST00000329493.6	c.322+13_322+18dup		splice_region_variant, intron_variant		2	NM_001135580.2	P1
MFSD12	ENST00000398558.8	c.331-504_331-503insGGGGGG		intron_variant		2
MFSD12	ENST00000615073.4	c.490+1328_490+1329insGGGGGG		intron_variant		3
TEKTIP1	ENST00000681976.1	c.163+13_163+18dup		splice_region_variant, intron_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 51 AN: 123128 Hom.: 1 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000159

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000846

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000395 AC: 48 AN: 1215556 Hom.: 0 Cov.: 0 AF XY: 0.0000317 AC XY: 19 AN XY: 599416

Gnomad4 AFR exome AF: 0.000213

Gnomad4 AMR exome AF: 0.000121

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000296

Gnomad4 SAS exome AF: 0.0000980

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000289

Gnomad4 OTH exome AF: 0.0000581

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000414 AC: 51 AN: 123144 Hom.: 1 Cov.: 0 AF XY: 0.000473 AC XY: 28 AN XY: 59166

Gnomad4 AFR AF: 0.00147

Gnomad4 AMR AF: 0.000159

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000846

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34196068; hg19: chr19-3543478;