rs2115200

chr6-39149922-T-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 0.169 in 152,100 control chromosomes in the GnomAD database, including 2,623 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 0.17 (2623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 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: 0.169 AC: 25748 AN: 151982 Hom.: 2621 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.169 AC: 25749 AN: 152100 Hom.: 2623 Cov.: 32 AF XY: 0.169 AC XY: 12559 AN XY: 74344

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.163

Alfa AF: 0.221 Hom.: 1740

Bravo AF: 0.164

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2115200; hg19: chr6-39117698;