rs2327949

Variant names:

• chr6-16110214-G-A
• rs2327949

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 0.216 in 152,152 control chromosomes in the GnomAD database, including 3,781 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 (3781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 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: 0.216 AC: 32798 AN: 152034 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.216 AC: 32818 AN: 152152 Hom.: 3781 Cov.: 32 AF XY: 0.218 AC XY: 16184 AN XY: 74358

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.184

Alfa AF: 0.235 Hom.: 5994

Bravo AF: 0.213

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2327949; hg19: chr6-16110445;