9-5182159-C-T

Variant summary

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

The NM_007179.3(INSL6):​c.289+3155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,794 control chromosomes in the GnomAD database, including 12,365 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 0.38 ( 12365 hom., cov: 31)

Consequence

INSL6
NM_007179.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.115
Variant links:
Genes affected
INSL6 (HGNC:6089): (insulin like 6) The protein encoded by this gene contains a classical signature of the insulin superfamily and is significantly similar to relaxin and relaxin-like factor. This gene is preferentially expressed in testis. Its expression in testis is restricted to interstitial cells surrounding seminiferous tubules, which suggests a role in sperm development and fertilization. [provided by RefSeq, Jul 2008]

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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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
INSL6NM_007179.3 linkc.289+3155G>A intron_variant Intron 1 of 1 ENST00000381641.4 NP_009110.2 Q9Y581
INSL6XM_011517702.4 linkc.289+3155G>A intron_variant Intron 1 of 2 XP_011516004.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
INSL6ENST00000381641.4 linkc.289+3155G>A intron_variant Intron 1 of 1 1 NM_007179.3 ENSP00000371054.3 Q9Y581
INSL6ENST00000649639.1 linkc.289+3155G>A intron_variant Intron 1 of 3 ENSP00000497955.1 A0A3B3ITZ2

Frequencies

GnomAD3 genomes
AF:
0.379
AC:
57501
AN:
151676
Hom.:
12344
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.599
Gnomad AMI
AF:
0.286
Gnomad AMR
AF:
0.339
Gnomad ASJ
AF:
0.253
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.308
Gnomad FIN
AF:
0.343
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.348
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.379
AC:
57566
AN:
151794
Hom.:
12365
Cov.:
31
AF XY:
0.379
AC XY:
28104
AN XY:
74176
show subpopulations
Gnomad4 AFR
AF:
0.599
Gnomad4 AMR
AF:
0.339
Gnomad4 ASJ
AF:
0.253
Gnomad4 EAS
AF:
0.256
Gnomad4 SAS
AF:
0.308
Gnomad4 FIN
AF:
0.343
Gnomad4 NFE
AF:
0.284
Gnomad4 OTH
AF:
0.349
Alfa
AF:
0.282
Hom.:
2764
Bravo
AF:
0.384
Asia WGS
AF:
0.321
AC:
1113
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.6
DANN
Benign
0.49

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: rs10974993; hg19: chr9-5182159; COSMIC: COSV67562729; API