rs2001114

Positions:

• chr6-167073090-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 0.333 in 151,962 control chromosomes in the GnomAD database, including 9,122 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 0.33 (9122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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: 0.333 AC: 50534 AN: 151844 Hom.: 9126 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.333 AC: 50536 AN: 151962 Hom.: 9122 Cov.: 32 AF XY: 0.332 AC XY: 24688 AN XY: 74282

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.337

Alfa AF: 0.350 Hom.: 1607

Bravo AF: 0.320

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001114; hg19: chr6-167486578;