NM_001135580.2:c.322+14_322+18delCCCCC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001135580.2(TEKTIP1):​c.322+14_322+18delCCCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,338,738 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00085 ( 2 hom., cov: 0)
Exomes 𝑓: 0.000077 ( 1 hom. )

Consequence

TEKTIP1
NM_001135580.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.478

Publications

3 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TEKTIP1NM_001135580.2 linkc.322+14_322+18delCCCCC intron_variant Intron 2 of 3 ENST00000329493.6 NP_001129052.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TEKTIP1ENST00000329493.6 linkc.322+8_322+12delCCCCC splice_region_variant, intron_variant Intron 2 of 3 2 NM_001135580.2 ENSP00000327950.4 A6NCJ1

Frequencies

GnomAD3 genomes
AF:
0.000845
AC:
104
AN:
123130
Hom.:
2
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00335
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000239
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:
0.0000169
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000765
AC:
93
AN:
1215592
Hom.:
1
AF XY:
0.0000667
AC XY:
40
AN XY:
599432
show subpopulations
African (AFR)
AF:
0.00266
AC:
75
AN:
28154
American (AMR)
AF:
0.000303
AC:
10
AN:
33012
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22134
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33838
South Asian (SAS)
AF:
0.0000280
AC:
2
AN:
71462
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
37934
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3624
European-Non Finnish (NFE)
AF:
0.00000214
AC:
2
AN:
933776
Other (OTH)
AF:
0.0000774
AC:
4
AN:
51658
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.649
Heterozygous variant carriers
0
4
9
13
18
22
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000853
AC:
105
AN:
123146
Hom.:
2
Cov.:
0
AF XY:
0.000794
AC XY:
47
AN XY:
59168
show subpopulations
African (AFR)
AF:
0.00337
AC:
101
AN:
29928
American (AMR)
AF:
0.000239
AC:
3
AN:
12568
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3092
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4642
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3650
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
7600
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
206
European-Non Finnish (NFE)
AF:
0.0000169
AC:
1
AN:
59082
Other (OTH)
AF:
0.00
AC:
0
AN:
1660
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.646
Heterozygous variant carriers
0
5
11
16
22
27
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.48
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs34196068; hg19: chr19-3543478; API