6-50249119-C-T

Variant names:

• chr6-50249119-C-T
• rs1417507

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 0.248 in 151,880 control chromosomes in the GnomAD database, including 5,124 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 0.25 (5124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.248 AC: 37696 AN: 151762 Hom.: 5113 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.248 AC: 37730 AN: 151880 Hom.: 5124 Cov.: 32 AF XY: 0.251 AC XY: 18631 AN XY: 74170

African (AFR) AF: 0.160 AC: 6644 AN: 41452

American (AMR) AF: 0.336 AC: 5131 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3472

East Asian (EAS) AF: 0.433 AC: 2230 AN: 5152

South Asian (SAS) AF: 0.195 AC: 937 AN: 4810

European-Finnish (FIN) AF: 0.313 AC: 3280 AN: 10490

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17739 AN: 67922

Other (OTH) AF: 0.249 AC: 525 AN: 2110

Alfa AF: 0.149 Hom.: 291

Bravo AF: 0.252

Asia WGS AF: 0.322 AC: 1114 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs1417507; hg19: chr6-50216832;