6-16124329-T-C

Variant names:

• chr6-16124329-T-C
• rs6459450

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 0.464 in 152,112 control chromosomes in the GnomAD database, including 18,376 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 0.46 (18376 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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: 0.463 AC: 70382 AN: 151994 Hom.: 18321 Cov.: 33

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.464 AC: 70507 AN: 152112 Hom.: 18376 Cov.: 33 AF XY: 0.466 AC XY: 34650 AN XY: 74340

African (AFR) AF: 0.658 AC: 27283 AN: 41464

American (AMR) AF: 0.529 AC: 8087 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3472

East Asian (EAS) AF: 0.804 AC: 4170 AN: 5184

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4822

European-Finnish (FIN) AF: 0.354 AC: 3735 AN: 10558

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22272 AN: 68004

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.386 Hom.: 34261

Bravo AF: 0.486

Asia WGS AF: 0.663 AC: 2304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs6459450; hg19: chr6-16124560;