rs8101509

Variant names:

• chr19-51905573-T-G
• rs8101509

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.395

Alfa AF: 0.338 Hom.: 2299

Bravo AF: 0.404

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs8101509; hg19: chr19-52408826;