chr9-5148278-C-T

Position:

• chr9-5148278-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649639.1(INSL6):​c.377-14686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,918 control chromosomes in the GnomAD database, including 14,433 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 0.40 (14433 hom., cov: 32)
• Consequence: INSL6 ENST00000649639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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]

INSL6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INSL6	XM_011517702.4	c.376+15901G>A		intron_variant			XP_011516004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INSL6	ENST00000649639.1	c.377-14686G>A		intron_variant				ENSP00000497955.1
INSL6	ENST00000510407.1	n.74-14686G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60876 AN: 151800 Hom.: 14404 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.363

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.401 AC: 60960 AN: 151918 Hom.: 14433 Cov.: 32 AF XY: 0.401 AC XY: 29767 AN XY: 74264

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.364

Alfa AF: 0.318 Hom.: 4897

Bravo AF: 0.409

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10118930; hg19: chr9-5148278;