rs1007026

Variant names:

• chr6-40071292-T-A
• rs1007026

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 0.184 in 152,126 control chromosomes in the GnomAD database, including 2,851 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 0.18 (2851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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: 0.184 AC: 27974 AN: 152008 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.184 AC: 28009 AN: 152126 Hom.: 2851 Cov.: 32 AF XY: 0.188 AC XY: 13984 AN XY: 74374

African (AFR) AF: 0.226 AC: 9357 AN: 41486

American (AMR) AF: 0.262 AC: 4009 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3472

East Asian (EAS) AF: 0.170 AC: 880 AN: 5176

South Asian (SAS) AF: 0.334 AC: 1606 AN: 4806

European-Finnish (FIN) AF: 0.152 AC: 1610 AN: 10584

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9429 AN: 67992

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.155 Hom.: 236

Bravo AF: 0.192

Asia WGS AF: 0.271 AC: 938 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1007026; hg19: chr6-40039031;