rs2207139

Variant names:

• chr6-50877777-A-G
• rs2207139

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 0.164 in 152,080 control chromosomes in the GnomAD database, including 2,316 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 0.16 (2316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 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: 0.164 AC: 24897 AN: 151964 Hom.: 2317 Cov.: 32

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.164 AC: 24902 AN: 152080 Hom.: 2316 Cov.: 32 AF XY: 0.166 AC XY: 12354 AN XY: 74326

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.168

Alfa AF: 0.188 Hom.: 395

Bravo AF: 0.168

Asia WGS AF: 0.225 AC: 783 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.45
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207139; hg19: chr6-50845490;