rs6511939

Positions:

• chr19-14573613-G-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 0.0971 in 151,806 control chromosomes in the GnomAD database, including 982 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 0.097 (982 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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 = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14721 AN: 151694 Hom.: 981 Cov.: 29

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.0874

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

GnomAD4 genome AF: 0.0971 AC: 14746 AN: 151806 Hom.: 982 Cov.: 29 AF XY: 0.0953 AC XY: 7070 AN XY: 74188

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0957

Gnomad4 FIN AF: 0.0553

Gnomad4 NFE AF: 0.0636

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0738 Hom.: 263

Bravo AF: 0.0985

Asia WGS AF: 0.0670 AC: 232 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	3.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6511939; hg19: chr19-14684425;