chr9-134919395-A-G

Variant names:

• chr9-134919395-A-G
• rs7857015

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 0.275 in 152,212 control chromosomes in the GnomAD database, including 6,289 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 0.27 (6289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 6 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 = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41851 AN: 152094 Hom.: 6291 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.275 AC: 41840 AN: 152212 Hom.: 6289 Cov.: 33 AF XY: 0.274 AC XY: 20356 AN XY: 74424

African (AFR) AF: 0.166 AC: 6888 AN: 41536

American (AMR) AF: 0.236 AC: 3608 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3468

East Asian (EAS) AF: 0.120 AC: 621 AN: 5188

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4824

European-Finnish (FIN) AF: 0.371 AC: 3925 AN: 10586

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23516 AN: 68000

Other (OTH) AF: 0.273 AC: 577 AN: 2112

Alfa AF: 0.287 Hom.: 991

Bravo AF: 0.261

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.31
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7857015; hg19: chr9-137811241;