rs9368649

Variant names:

• chr6-30971106-A-G
• rs9368649

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 0.107 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
• Publications: 23 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 = 0.318 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

African (AFR) AF: 0.0289 AC: 1202 AN: 41556

American (AMR) AF: 0.0799 AC: 1223 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1708 AN: 5154

South Asian (SAS) AF: 0.203 AC: 981 AN: 4832

European-Finnish (FIN) AF: 0.147 AC: 1561 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8744 AN: 68018

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.116 Hom.: 4039

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9368649; hg19: chr6-30938883;