6-106334021-G-T

Variant names:

• chr6-106334021-G-T
• rs2355380

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.498 AC: 20617 AN: 41374

American (AMR) AF: 0.686 AC: 10468 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2173 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3216 AN: 5144

South Asian (SAS) AF: 0.692 AC: 3340 AN: 4824

European-Finnish (FIN) AF: 0.693 AC: 7292 AN: 10528

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45252 AN: 67960

Other (OTH) AF: 0.618 AC: 1301 AN: 2104

Alfa AF: 0.638 Hom.: 16542

Bravo AF: 0.616

Asia WGS AF: 0.598 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.49
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2355380; hg19: chr6-106781896;