rs9368649

Variant names:

• chr6-30971106-A-G
• rs9368649

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 0.107 in 152,252 control chromosomes in the GnomAD database, including 1,218 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 0.11 (1218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

ACMG classification

Verdict is Benign. Variant got -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 = 0.318 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: 0.107 AC: 16266 AN: 152134 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.107 AC: 16256 AN: 152252 Hom.: 1218 Cov.: 32 AF XY: 0.111 AC XY: 8240 AN XY: 74434

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.0952

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.124 Hom.: 1586

Bravo AF: 0.0965

Asia WGS AF: 0.214 AC: 746 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	5.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9368649; hg19: chr6-30938883;