chr9-85154270-A-G

Variant names:

• chr9-85154270-A-G
• rs1931101

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 0.17 in 152,060 control chromosomes in the GnomAD database, including 3,033 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 0.17 (3033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25754 AN: 151942 Hom.: 3031 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0808

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.170 AC: 25781 AN: 152060 Hom.: 3033 Cov.: 32 AF XY: 0.167 AC XY: 12445 AN XY: 74328

African (AFR) AF: 0.336 AC: 13920 AN: 41438

American (AMR) AF: 0.0925 AC: 1413 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0808 AC: 280 AN: 3464

East Asian (EAS) AF: 0.0477 AC: 247 AN: 5182

South Asian (SAS) AF: 0.164 AC: 789 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1196 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7490 AN: 67992

Other (OTH) AF: 0.140 AC: 296 AN: 2108

Alfa AF: 0.123 Hom.: 1967

Bravo AF: 0.175

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.50
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1931101; hg19: chr9-87769185;