rs7006032

Variant names:

• chr8-139246954-C-T
• rs7006032

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 0.368 in 151,540 control chromosomes in the GnomAD database, including 11,209 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 0.37 (11209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55794 AN: 151422 Hom.: 11197 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.368 AC: 55816 AN: 151540 Hom.: 11209 Cov.: 32 AF XY: 0.372 AC XY: 27546 AN XY: 74070

African (AFR) AF: 0.229 AC: 9409 AN: 41024

American (AMR) AF: 0.476 AC: 7262 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1198 AN: 5166

South Asian (SAS) AF: 0.336 AC: 1615 AN: 4812

European-Finnish (FIN) AF: 0.464 AC: 4894 AN: 10552

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28921 AN: 67958

Other (OTH) AF: 0.351 AC: 737 AN: 2100

Alfa AF: 0.409 Hom.: 6563

Bravo AF: 0.360

Asia WGS AF: 0.286 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.86
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7006032; hg19: chr8-140259197;