rs228907

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001374504.1(TMPRSS6):​c.202+1663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,792 control chromosomes in the GnomAD database, including 8,352 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8352 hom., cov: 31)

Consequence

TMPRSS6
NM_001374504.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.850
Variant links:
Genes affected
TMPRSS6 (HGNC:16517): (transmembrane serine protease 6) The protein encoded by this gene is a type II transmembrane serine proteinase that is found attached to the cell surface. The encoded protein may be involved in matrix remodeling processes in the liver. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TMPRSS6NM_001374504.1 linkuse as main transcriptc.202+1663C>T intron_variant ENST00000676104.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TMPRSS6ENST00000676104.1 linkuse as main transcriptc.202+1663C>T intron_variant NM_001374504.1 P1Q8IU80-1

Frequencies

GnomAD3 genomes
AF:
0.326
AC:
49382
AN:
151674
Hom.:
8337
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.393
Gnomad AMI
AF:
0.164
Gnomad AMR
AF:
0.304
Gnomad ASJ
AF:
0.214
Gnomad EAS
AF:
0.431
Gnomad SAS
AF:
0.409
Gnomad FIN
AF:
0.296
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.326
AC:
49442
AN:
151792
Hom.:
8352
Cov.:
31
AF XY:
0.326
AC XY:
24180
AN XY:
74184
show subpopulations
Gnomad4 AFR
AF:
0.393
Gnomad4 AMR
AF:
0.305
Gnomad4 ASJ
AF:
0.214
Gnomad4 EAS
AF:
0.430
Gnomad4 SAS
AF:
0.409
Gnomad4 FIN
AF:
0.296
Gnomad4 NFE
AF:
0.289
Gnomad4 OTH
AF:
0.307
Alfa
AF:
0.278
Hom.:
8640
Bravo
AF:
0.322
Asia WGS
AF:
0.449
AC:
1562
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.7
DANN
Benign
0.80

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs228907; hg19: chr22-37497593; API