rs6506640

Variant names:

• chr18-9099202-G-A
• rs6506640

Your query was ambiguous. Multiple possible variants found:

• chr18-9099202-G-A
• chr18-9099202-G-C
• chr18-9099202-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.82 in 152,100 control chromosomes in the GnomAD database, including 51,221 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 0.82 (51221 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 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: 0.820 AC: 124586 AN: 151982 Hom.: 51177 Cov.: 30

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.820 AC: 124682 AN: 152100 Hom.: 51221 Cov.: 30 AF XY: 0.817 AC XY: 60707 AN XY: 74344

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.836

Alfa AF: 0.785 Hom.: 2371

Bravo AF: 0.818

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6506640; hg19: chr18-9099200;