rs1036107

Variant names:

• chr9-23677966-A-C
• rs1036107

Your query was ambiguous. Multiple possible variants found:

• chr9-23677966-A-C
• chr9-23677966-A-T

Variant summary

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

The variant allele was found at a frequency of 0.676 in 151,996 control chromosomes in the GnomAD database, including 35,821 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 0.68 (35821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102646 AN: 151878 Hom.: 35811 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.676 AC: 102685 AN: 151996 Hom.: 35821 Cov.: 32 AF XY: 0.681 AC XY: 50560 AN XY: 74280

African (AFR) AF: 0.492 AC: 20369 AN: 41440

American (AMR) AF: 0.772 AC: 11776 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2660 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4611 AN: 5154

South Asian (SAS) AF: 0.782 AC: 3766 AN: 4818

European-Finnish (FIN) AF: 0.760 AC: 8034 AN: 10572

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49169 AN: 67968

Other (OTH) AF: 0.678 AC: 1429 AN: 2108

Alfa AF: 0.711 Hom.: 84167

Bravo AF: 0.668

Asia WGS AF: 0.818 AC: 2842 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.7
DANN	Benign	0.75
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1036107; hg19: chr9-23677964;