rs8101509

Variant names:

• chr19-51905573-T-G
• rs8101509

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 0.402 in 151,990 control chromosomes in the GnomAD database, including 14,273 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 (14273 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.402 AC: 61061 AN: 151872 Hom.: 14229 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.402 AC: 61167 AN: 151990 Hom.: 14273 Cov.: 31 AF XY: 0.406 AC XY: 30176 AN XY: 74276

African (AFR) AF: 0.645 AC: 26745 AN: 41444

American (AMR) AF: 0.311 AC: 4755 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1494 AN: 5156

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3730 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19269 AN: 67962

Other (OTH) AF: 0.395 AC: 834 AN: 2112

Alfa AF: 0.344 Hom.: 2439

Bravo AF: 0.404

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8101509; hg19: chr19-52408826;