rs9398918

Variant names:

• chr6-129724532-G-A
• rs9398918

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 0.19 in 152,048 control chromosomes in the GnomAD database, including 2,894 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 (2894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 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: 0.190 AC: 28924 AN: 151930 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.190 AC: 28952 AN: 152048 Hom.: 2894 Cov.: 32 AF XY: 0.190 AC XY: 14129 AN XY: 74336

African (AFR) AF: 0.168 AC: 6947 AN: 41460

American (AMR) AF: 0.152 AC: 2312 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5174

South Asian (SAS) AF: 0.153 AC: 736 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2029 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14182 AN: 67974

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.204 Hom.: 13685

Bravo AF: 0.188

Asia WGS AF: 0.164 AC: 568 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	0.76
DANN	Benign	0.67
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs9398918; hg19: chr6-130045677;