rs1359885

Variant names:

• chr9-36126330-C-G
• rs1359885
• ENST00000753762.1:n.195-12251G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-36126330-C-G
• chr9-36126330-C-T

Variant summary

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

The ENST00000753762.1(ENSG00000298190):​n.195-12251G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,034 control chromosomes in the GnomAD database, including 30,941 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 0.64 (30941 hom., cov: 32)
• Consequence: ENSG00000298190 ENST00000753762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 2 publications found

Genes affected

ENSG00000298190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298190	ENST00000753762.1	n.195-12251G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96700 AN: 151914 Hom.: 30894 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.637 AC: 96808 AN: 152034 Hom.: 30941 Cov.: 32 AF XY: 0.641 AC XY: 47621 AN XY: 74332

African (AFR) AF: 0.654 AC: 27099 AN: 41458

American (AMR) AF: 0.578 AC: 8833 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2529 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3825 AN: 5156

South Asian (SAS) AF: 0.738 AC: 3559 AN: 4820

European-Finnish (FIN) AF: 0.638 AC: 6736 AN: 10554

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42088 AN: 67986

Other (OTH) AF: 0.667 AC: 1409 AN: 2112

Alfa AF: 0.616 Hom.: 3584

Bravo AF: 0.630

Asia WGS AF: 0.716 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1359885; hg19: chr9-36126327;