19-3543480-GCCCCCC-GCCCCCCCCCCC

Variant names:

• chr19-3543480-G-GCCCCC
• rs34196068
• NM_001135580.2:c.322+14_322+18dupCCCCC

Variant summary

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

The ENST00000329493.6(TEKTIP1):​c.322+7_322+8insCCCCC 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 0.0022 (19 hom., cov: 0)
  • Exomes 𝑓: 0.00015 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEKTIP1 ENST00000329493.6 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 rank	MANE	Protein	UniProt
TEKTIP1	NM_001135580.2	c.322+14_322+18dupCCCCC		intron_variant	Intron 2 of 3	ENST00000329493.6	NP_001129052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKTIP1	ENST00000329493.6	c.322+7_322+8insCCCCC		splice_region_variant, intron_variant	Intron 2 of 3	2	NM_001135580.2	ENSP00000327950.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 276 AN: 123110 Hom.: 19 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00747

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000558

Gnomad ASJ AF: 0.000647

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000273

Gnomad FIN AF: 0.000658

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000609

Gnomad OTH AF: 0.00121

GnomAD4 exome AF: 0.000151 AC: 183 AN: 1215440 Hom.: 0 Cov.: 0 AF XY: 0.000125 AC XY: 75 AN XY: 599352

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.000182

Gnomad4 ASJ exome AF: 0.0000904

Gnomad4 EAS exome AF: 0.0000296

Gnomad4 SAS exome AF: 0.000294

Gnomad4 FIN exome AF: 0.0000791

Gnomad4 NFE exome AF: 0.000109

Gnomad4 OTH exome AF: 0.000232

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00224 AC: 276 AN: 123126 Hom.: 19 Cov.: 0 AF XY: 0.00220 AC XY: 130 AN XY: 59158

Gnomad4 AFR AF: 0.00745

Gnomad4 AMR AF: 0.000557

Gnomad4 ASJ AF: 0.000647

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000274

Gnomad4 FIN AF: 0.000658

Gnomad4 NFE AF: 0.000609

Gnomad4 OTH AF: 0.00120

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;