6-6129985-G-T

Variant names:

• chr6-6129985-G-T
• rs2326699

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 0.339 in 152,046 control chromosomes in the GnomAD database, including 10,455 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 0.34 (10455 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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: 0.338 AC: 51396 AN: 151928 Hom.: 10429 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.339 AC: 51475 AN: 152046 Hom.: 10455 Cov.: 33 AF XY: 0.338 AC XY: 25085 AN XY: 74316

African (AFR) AF: 0.579 AC: 24010 AN: 41462

American (AMR) AF: 0.255 AC: 3887 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1580 AN: 5178

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4822

European-Finnish (FIN) AF: 0.278 AC: 2937 AN: 10564

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15982 AN: 67966

Other (OTH) AF: 0.292 AC: 614 AN: 2106

Alfa AF: 0.264 Hom.: 7238

Bravo AF: 0.349

Asia WGS AF: 0.314 AC: 1090 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	0.89
DANN	Benign	0.12
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2326699; hg19: chr6-6130218;