NM_001135580.2:c.322+18delC

Variant names:

• chr19-3543480-GC-G
• rs34196068
• NM_001135580.2:c.322+18delC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001135580.2(TEKTIP1):​c.322+18delC 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 0.034 (247 hom., cov: 0)
  • Exomes 𝑓: 0.17 (274 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.097 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKTIP1	NM_001135580.2	c.322+18delC		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+8delC		splice_region_variant, intron_variant	Intron 2 of 3	2	NM_001135580.2	ENSP00000327950.4

Frequencies

GnomAD3 genomes AF: 0.0339 AC: 4160 AN: 122714 Hom.: 245 Cov.: 0

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.00418

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.0178

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.00805

Gnomad MID AF: 0.0310

Gnomad NFE AF: 0.00818

Gnomad OTH AF: 0.0298

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.168 AC: 171103 AN: 1020834 Hom.: 274 Cov.: 0 AF XY: 0.170 AC XY: 85562 AN XY: 503588

Gnomad4 AFR exome AF: 0.162

Gnomad4 AMR exome AF: 0.198

Gnomad4 ASJ exome AF: 0.182

Gnomad4 EAS exome AF: 0.371

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.225

Gnomad4 NFE exome AF: 0.159

Gnomad4 OTH exome AF: 0.180

GnomAD4 genome AF: 0.0340 AC: 4167 AN: 122728 Hom.: 247 Cov.: 0 AF XY: 0.0349 AC XY: 2055 AN XY: 58916

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0192

Gnomad4 ASJ AF: 0.0178

Gnomad4 EAS AF: 0.0170

Gnomad4 SAS AF: 0.0546

Gnomad4 FIN AF: 0.00805

Gnomad4 NFE AF: 0.00820

Gnomad4 OTH AF: 0.0296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34196068; hg19: chr19-3543478;