chr8-56266648-T-A

Variant names:

• chr8-56266648-T-A
• rs7837540

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 0.401 in 151,906 control chromosomes in the GnomAD database, including 12,687 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 0.40 (12687 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.401 AC: 60881 AN: 151788 Hom.: 12652 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.401 AC: 60962 AN: 151906 Hom.: 12687 Cov.: 31 AF XY: 0.399 AC XY: 29657 AN XY: 74256

African (AFR) AF: 0.515 AC: 21294 AN: 41382

American (AMR) AF: 0.318 AC: 4848 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1254 AN: 5164

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4818

European-Finnish (FIN) AF: 0.437 AC: 4617 AN: 10572

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25201 AN: 67916

Other (OTH) AF: 0.376 AC: 795 AN: 2112

Alfa AF: 0.229 Hom.: 478

Bravo AF: 0.399

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.40
DANN	Benign	0.28
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs7837540; hg19: chr8-57179207;