NM_001135580.2:c.322+15_322+18dupCCCC

Variant names:

• chr19-3543480-G-GCCCC
• rs34196068
• NM_001135580.2:c.322+15_322+18dupCCCC

Variant summary

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

The NM_001135580.2(TEKTIP1):​c.322+15_322+18dupCCCC variant causes a 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 0.0079 (37 hom., cov: 0)
  • Exomes 𝑓: 0.00048 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEKTIP1 NM_001135580.2 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+15_322+18dupCCCC		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+8insCCCC		splice_region_variant, intron_variant	Intron 2 of 3	2	NM_001135580.2	ENSP00000327950.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 967 AN: 123072 Hom.: 37 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.00279

Gnomad AMR AF: 0.00287

Gnomad ASJ AF: 0.00291

Gnomad EAS AF: 0.000215

Gnomad SAS AF: 0.00273

Gnomad FIN AF: 0.00224

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00401

Gnomad OTH AF: 0.00363

GnomAD4 exome AF: 0.000482 AC: 586 AN: 1214996 Hom.: 0 Cov.: 0 AF XY: 0.000474 AC XY: 284 AN XY: 599150

Gnomad4 AFR exome AF: 0.00342

Gnomad4 AMR exome AF: 0.000394

Gnomad4 ASJ exome AF: 0.000316

Gnomad4 EAS exome AF: 0.0000591

Gnomad4 SAS exome AF: 0.000490

Gnomad4 FIN exome AF: 0.0000791

Gnomad4 NFE exome AF: 0.000426

Gnomad4 OTH exome AF: 0.000542

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00786 AC: 967 AN: 123088 Hom.: 37 Cov.: 0 AF XY: 0.00719 AC XY: 425 AN XY: 59140

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.00287

Gnomad4 ASJ AF: 0.00291

Gnomad4 EAS AF: 0.000215

Gnomad4 SAS AF: 0.00274

Gnomad4 FIN AF: 0.00224

Gnomad4 NFE AF: 0.00401

Gnomad4 OTH AF: 0.00361

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;