8-11570886-C-T

Variant names:

• chr8-11570886-C-T
• rs11991139

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 0.349 in 152,124 control chromosomes in the GnomAD database, including 10,934 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 0.35 (10934 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 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: 0.349 AC: 53069 AN: 152006 Hom.: 10935 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.349 AC: 53066 AN: 152124 Hom.: 10934 Cov.: 33 AF XY: 0.339 AC XY: 25218 AN XY: 74360

African (AFR) AF: 0.176 AC: 7301 AN: 41520

American (AMR) AF: 0.313 AC: 4789 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5180

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4818

European-Finnish (FIN) AF: 0.373 AC: 3945 AN: 10570

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32617 AN: 67956

Other (OTH) AF: 0.366 AC: 772 AN: 2112

Alfa AF: 0.416 Hom.: 5214

Bravo AF: 0.333

Asia WGS AF: 0.155 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11991139; hg19: chr8-11428395;