9-135348041-A-G

Variant names:

• chr9-135348041-A-G
• rs6538018

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 0.395 in 151,958 control chromosomes in the GnomAD database, including 13,240 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 0.40 (13240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59973 AN: 151838 Hom.: 13216 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.395 AC: 60050 AN: 151958 Hom.: 13240 Cov.: 32 AF XY: 0.389 AC XY: 28917 AN XY: 74274

African (AFR) AF: 0.611 AC: 25341 AN: 41444

American (AMR) AF: 0.323 AC: 4940 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1991 AN: 5160

South Asian (SAS) AF: 0.397 AC: 1904 AN: 4802

European-Finnish (FIN) AF: 0.248 AC: 2620 AN: 10562

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21219 AN: 67930

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.343 Hom.: 21462

Bravo AF: 0.409

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6538018; hg19: chr9-138239887;