rs700085

Variant names:

• chr9-123108187-T-C
• rs700085

Your query was ambiguous. Multiple possible variants found:

• chr9-123108187-T-C
• chr9-123108187-T-G

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 0.726 in 152,112 control chromosomes in the GnomAD database, including 46,951 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 0.73 (46951 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.912 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: 0.727 AC: 110446 AN: 151994 Hom.: 46951 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.726 AC: 110459 AN: 152112 Hom.: 46951 Cov.: 31 AF XY: 0.732 AC XY: 54476 AN XY: 74382

African (AFR) AF: 0.245 AC: 10131 AN: 41428

American (AMR) AF: 0.860 AC: 13164 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3146 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4700 AN: 5162

South Asian (SAS) AF: 0.918 AC: 4422 AN: 4816

European-Finnish (FIN) AF: 0.919 AC: 9746 AN: 10608

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62432 AN: 68014

Other (OTH) AF: 0.776 AC: 1634 AN: 2106

Alfa AF: 0.846 Hom.: 169076

Bravo AF: 0.700

Asia WGS AF: 0.860 AC: 2990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs700085; hg19: chr9-125870466;