rs2207139

Positions:

• chr6-50877777-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;