rs786100

chr6-122241607-G-T

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 0.234 in 151,636 control chromosomes in the GnomAD database, including 4,796 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 0.23 (4796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 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: 0.235 AC: 35552 AN: 151514 Hom.: 4795 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.234 AC: 35545 AN: 151636 Hom.: 4796 Cov.: 32 AF XY: 0.229 AC XY: 16989 AN XY: 74134

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.247

Alfa AF: 0.263 Hom.: 706

Bravo AF: 0.234

Asia WGS AF: 0.251 AC: 872 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs786100; hg19: chr6-122562753;