6-31579834-C-T

Variant names:

• chr6-31579834-C-T
• rs769177

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 0.028 in 152,268 control chromosomes in the GnomAD database, including 108 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 0.028 (108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0713 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: 0.0280 AC: 4265 AN: 152150 Hom.: 108 Cov.: 32

Gnomad AFR AF: 0.00864

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.0769

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0280 AC: 4266 AN: 152268 Hom.: 108 Cov.: 32 AF XY: 0.0308 AC XY: 2292 AN XY: 74438

African (AFR) AF: 0.00859 AC: 357 AN: 41564

American (AMR) AF: 0.0199 AC: 305 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.0765 AC: 396 AN: 5178

South Asian (SAS) AF: 0.0777 AC: 375 AN: 4824

European-Finnish (FIN) AF: 0.0709 AC: 752 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0261 AC: 1774 AN: 67998

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0289 Hom.: 283

Bravo AF: 0.0219

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.72
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs769177; hg19: chr6-31547611;