rs8113007

Variant names:

• chr19-39252463-A-T
• rs8113007

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 0.285 in 152,166 control chromosomes in the GnomAD database, including 6,454 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 0.28 (6454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 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: 0.285 AC: 43296 AN: 152048 Hom.: 6448 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.285 AC: 43343 AN: 152166 Hom.: 6454 Cov.: 32 AF XY: 0.279 AC XY: 20731 AN XY: 74404

African (AFR) AF: 0.298 AC: 12350 AN: 41498

American (AMR) AF: 0.341 AC: 5216 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.0715 AC: 371 AN: 5192

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4824

European-Finnish (FIN) AF: 0.212 AC: 2242 AN: 10586

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19766 AN: 67998

Other (OTH) AF: 0.294 AC: 622 AN: 2114

Alfa AF: 0.298 Hom.: 841

Bravo AF: 0.298

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.87
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs8113007; hg19: chr19-39743103;