6-31050769-C-T

Variant names:

• chr6-31050769-C-T
• rs2523864

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 0.466 in 152,044 control chromosomes in the GnomAD database, including 17,257 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 0.47 (17257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.465 AC: 70716 AN: 151926 Hom.: 17220 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.466 AC: 70797 AN: 152044 Hom.: 17257 Cov.: 32 AF XY: 0.456 AC XY: 33922 AN XY: 74326

African (AFR) AF: 0.608 AC: 25208 AN: 41470

American (AMR) AF: 0.383 AC: 5860 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2136 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1673 AN: 5170

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4820

European-Finnish (FIN) AF: 0.311 AC: 3285 AN: 10556

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29084 AN: 67960

Other (OTH) AF: 0.492 AC: 1040 AN: 2112

Alfa AF: 0.446 Hom.: 51524

Bravo AF: 0.477

Asia WGS AF: 0.411 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.86
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs2523864; hg19: chr6-31018546;