rs7006278

Variant names:

• chr8-23660545-C-T
• rs7006278

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 0.258 in 152,032 control chromosomes in the GnomAD database, including 5,198 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 0.26 (5198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39148 AN: 151914 Hom.: 5197 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.258 AC: 39176 AN: 152032 Hom.: 5198 Cov.: 32 AF XY: 0.267 AC XY: 19862 AN XY: 74314

African (AFR) AF: 0.262 AC: 10883 AN: 41476

American (AMR) AF: 0.288 AC: 4402 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1498 AN: 5166

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4824

European-Finnish (FIN) AF: 0.364 AC: 3827 AN: 10518

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15209 AN: 67970

Other (OTH) AF: 0.258 AC: 543 AN: 2108

Alfa AF: 0.230 Hom.: 1739

Bravo AF: 0.250

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs7006278; hg19: chr8-23518058;