rs9349149

Variant names:

• chr6-40313134-C-T
• rs9349149

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 0.221 in 152,136 control chromosomes in the GnomAD database, including 4,140 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 0.22 (4140 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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: 0.221 AC: 33662 AN: 152018 Hom.: 4140 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.221 AC: 33659 AN: 152136 Hom.: 4140 Cov.: 33 AF XY: 0.224 AC XY: 16626 AN XY: 74362

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.240

Alfa AF: 0.241 Hom.: 809

Bravo AF: 0.208

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9349149; hg19: chr6-40280873;