rs9690040

Variant names:

• chr7-155294006-T-C
• rs9690040
• ENST00000743985.1:n.1130+2298A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000743985.1(INSIG1-DT):​n.1130+2298A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,086 control chromosomes in the GnomAD database, including 14,637 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 0.43 (14637 hom., cov: 33)
• Consequence: INSIG1-DT ENST00000743985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INSIG1-DT	NR_183446.1	n.1355+2298A>G		intron_variant	Intron 1 of 1
INSIG1-DT	NR_183447.1	n.830+4145A>G		intron_variant	Intron 1 of 1
INSIG1-DT	NR_183448.1	n.830+4145A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INSIG1-DT	ENST00000743985.1	n.1130+2298A>G		intron_variant	Intron 1 of 1
INSIG1-DT	ENST00000743986.1	n.707+2718A>G		intron_variant	Intron 1 of 1
INSIG1-DT	ENST00000743987.1	n.1147+2298A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65773 AN: 151970 Hom.: 14614 Cov.: 33

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.433 AC: 65834 AN: 152086 Hom.: 14637 Cov.: 33 AF XY: 0.431 AC XY: 32060 AN XY: 74362

African (AFR) AF: 0.547 AC: 22693 AN: 41470

American (AMR) AF: 0.343 AC: 5251 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3464

East Asian (EAS) AF: 0.481 AC: 2491 AN: 5180

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4820

European-Finnish (FIN) AF: 0.425 AC: 4503 AN: 10586

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26571 AN: 67962

Other (OTH) AF: 0.410 AC: 866 AN: 2110

Alfa AF: 0.398 Hom.: 22527

Bravo AF: 0.436

Asia WGS AF: 0.353 AC: 1227 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	0.25
DANN	Benign	0.46
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9690040; hg19: chr7-155085716;