rs6511939

Variant names:

• chr19-14573613-G-A
• rs6511939

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 0.0971 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.190 AC: 7855 AN: 41404

American (AMR) AF: 0.0595 AC: 907 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3468

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5176

South Asian (SAS) AF: 0.0957 AC: 461 AN: 4816

European-Finnish (FIN) AF: 0.0553 AC: 577 AN: 10436

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0636 AC: 4322 AN: 67962

Other (OTH) AF: 0.0875 AC: 184 AN: 2104

Alfa AF: 0.0736 Hom.: 284

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
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6511939; hg19: chr19-14684425;