rs1036107

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.678

Alfa AF: 0.716 Hom.: 50817

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1036107; hg19: chr9-23677964;