chr6-106334021-G-T

Position:

• chr6-106334021-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 0.622 in 151,878 control chromosomes in the GnomAD database, including 29,820 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 0.62 (29820 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.675 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: 0.622 AC: 94334 AN: 151760 Hom.: 29803 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.622 AC: 94401 AN: 151878 Hom.: 29820 Cov.: 31 AF XY: 0.625 AC XY: 46357 AN XY: 74206

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.618

Alfa AF: 0.637 Hom.: 14732

Bravo AF: 0.616

Asia WGS AF: 0.598 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2355380; hg19: chr6-106781896;