rs8102901

Positions:

• chr19-49049297-C-A

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 0.327 in 149,414 control chromosomes in the GnomAD database, including 7,996 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 0.33 (7996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 48812 AN: 149290 Hom.: 7995 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.327 AC: 48820 AN: 149414 Hom.: 7996 Cov.: 31 AF XY: 0.329 AC XY: 24055 AN XY: 73064

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.323

Alfa AF: 0.337 Hom.: 1083

Bravo AF: 0.324

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102901; hg19: chr19-49552554;