6-138126973-A-G

Position:

• chr6-138126973-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 0.248 in 152,130 control chromosomes in the GnomAD database, including 4,936 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 0.25 (4936 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37676 AN: 152012 Hom.: 4919 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.248 AC: 37727 AN: 152130 Hom.: 4936 Cov.: 33 AF XY: 0.244 AC XY: 18154 AN XY: 74372

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.271

Alfa AF: 0.264 Hom.: 2822

Bravo AF: 0.247

Asia WGS AF: 0.329 AC: 1145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.025
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12661926; hg19: chr6-138448110;