6-28553539-C-T

Variant names:

• chr6-28553539-C-T
• rs393414

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 0.311 in 151,452 control chromosomes in the GnomAD database, including 8,004 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 0.31 (8004 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47092 AN: 151332 Hom.: 7983 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.311 AC: 47164 AN: 151452 Hom.: 8004 Cov.: 31 AF XY: 0.315 AC XY: 23274 AN XY: 73980

African (AFR) AF: 0.429 AC: 17703 AN: 41220

American (AMR) AF: 0.320 AC: 4872 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2759 AN: 5134

South Asian (SAS) AF: 0.342 AC: 1632 AN: 4768

European-Finnish (FIN) AF: 0.273 AC: 2849 AN: 10452

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15429 AN: 67878

Other (OTH) AF: 0.301 AC: 634 AN: 2108

Alfa AF: 0.254 Hom.: 6612

Bravo AF: 0.321

Asia WGS AF: 0.379 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.66
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs393414; hg19: chr6-28521316;