Genetic Variant ENST00000609974.1:n.1509A>C (chr7-155296033-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000609974.1(INSIG1-DT):n.1509A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,278 control chromosomes in the GnomAD database, including 55,233 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 0.85 ( 55231 hom., cov: 33)

Exomes 𝑓: 0.75 ( 2 hom. )

Consequence

INSIG1-DT
ENST00000609974.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Variant links:

Genes affected

INSIG1-DT (HGNC:55155): (INSIG1 divergent transcript)

INSIG1-DT links:

Genome browser will be placed here

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 = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
INSIG1-DT	NR_183446.1 link	n.1355+271A>C	intron_variant	Intron 1 of 1
INSIG1-DT	NR_183447.1 link	n.830+2118A>C	intron_variant	Intron 1 of 1
INSIG1-DT	NR_183448.1 link	n.830+2118A>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INSIG1-DT	ENST00000609974.1 link	n.1509A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.850

AC:

129311

AN:

152152

Hom.:

55182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.902

Gnomad AMI

AF:

0.891

Gnomad AMR

AF:

0.820

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.727

Gnomad SAS

AF:

0.674

Gnomad FIN

AF:

0.860

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.848

Gnomad OTH

AF:

0.839

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

1.00

GnomAD4 genome

AF:

0.850

AC:

129420

AN:

152270

Hom.:

55231

Cov.:

AF XY:

0.846

AC XY:

62984

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.902

Gnomad4 AMR

AF:

0.820

Gnomad4 ASJ

AF:

0.791

Gnomad4 EAS

AF:

0.727

Gnomad4 SAS

AF:

0.673

Gnomad4 FIN

AF:

0.860

Gnomad4 NFE

AF:

0.848

Gnomad4 OTH

AF:

0.839

Alfa

AF:

0.862

Hom.:

8038

Bravo

AF:

0.852

Asia WGS

AF:

0.727

AC:

2526

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

0.87

DANN

Benign

0.47

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over