rs9488238

Variant names:

• chr6-113695931-A-G
• rs9488238

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 0.0438 in 152,300 control chromosomes in the GnomAD database, including 214 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 0.044 (214 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.088 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: 0.0437 AC: 6651 AN: 152182 Hom.: 213 Cov.: 33

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0181

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0438 AC: 6670 AN: 152300 Hom.: 214 Cov.: 33 AF XY: 0.0424 AC XY: 3155 AN XY: 74476

African (AFR) AF: 0.0904 AC: 3754 AN: 41542

American (AMR) AF: 0.0181 AC: 277 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3472

East Asian (EAS) AF: 0.0173 AC: 90 AN: 5190

South Asian (SAS) AF: 0.0267 AC: 129 AN: 4828

European-Finnish (FIN) AF: 0.0128 AC: 136 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2100 AN: 68024

Other (OTH) AF: 0.0293 AC: 62 AN: 2114

Alfa AF: 0.0373 Hom.: 335

Bravo AF: 0.0466

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.76
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs9488238; hg19: chr6-114017133;