chr9-117702447-G-A

Variant names:

• chr9-117702447-G-A
• rs1927914

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 0.531 in 152,050 control chromosomes in the GnomAD database, including 24,124 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 0.53 (24124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 158 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.532 AC: 80777 AN: 151932 Hom.: 24131 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.531 AC: 80786 AN: 152050 Hom.: 24124 Cov.: 32 AF XY: 0.530 AC XY: 39379 AN XY: 74326

African (AFR) AF: 0.234 AC: 9718 AN: 41492

American (AMR) AF: 0.614 AC: 9385 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3468

East Asian (EAS) AF: 0.619 AC: 3196 AN: 5162

South Asian (SAS) AF: 0.616 AC: 2969 AN: 4818

European-Finnish (FIN) AF: 0.551 AC: 5817 AN: 10550

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45418 AN: 67958

Other (OTH) AF: 0.579 AC: 1222 AN: 2110

Alfa AF: 0.631 Hom.: 20989

Bravo AF: 0.527

Asia WGS AF: 0.594 AC: 2067 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1927914; hg19: chr9-120464725;