rs9483788

Variant names:

• chr6-135114363-T-C
• rs9483788

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 0.194 in 152,144 control chromosomes in the GnomAD database, including 3,437 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 0.19 (3437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 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: 0.194 AC: 29553 AN: 152026 Hom.: 3437 Cov.: 32

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.194 AC: 29554 AN: 152144 Hom.: 3437 Cov.: 32 AF XY: 0.194 AC XY: 14462 AN XY: 74360

African (AFR) AF: 0.0757 AC: 3144 AN: 41532

American (AMR) AF: 0.177 AC: 2699 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1398 AN: 5176

South Asian (SAS) AF: 0.126 AC: 606 AN: 4816

European-Finnish (FIN) AF: 0.324 AC: 3421 AN: 10560

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17094 AN: 67990

Other (OTH) AF: 0.161 AC: 341 AN: 2116

Alfa AF: 0.234 Hom.: 14370

Bravo AF: 0.182

Asia WGS AF: 0.162 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9483788; hg19: chr6-135435501; COSMIC: COSV58836602;