6-15676246-G-C

Variant names:

• chr6-15676246-G-C
• rs17407828

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 0.232 in 152,120 control chromosomes in the GnomAD database, including 4,833 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 0.23 (4833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 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: 0.232 AC: 35315 AN: 152002 Hom.: 4826 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.232 AC: 35330 AN: 152120 Hom.: 4833 Cov.: 32 AF XY: 0.225 AC XY: 16730 AN XY: 74362

African (AFR) AF: 0.133 AC: 5523 AN: 41518

American (AMR) AF: 0.208 AC: 3171 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5180

South Asian (SAS) AF: 0.115 AC: 554 AN: 4820

European-Finnish (FIN) AF: 0.237 AC: 2508 AN: 10566

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21551 AN: 67972

Other (OTH) AF: 0.239 AC: 506 AN: 2114

Alfa AF: 0.268 Hom.: 725

Bravo AF: 0.228

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.41
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs17407828; hg19: chr6-15676477;