rs6509541

chr19-51448049-T-G

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 0.193 in 152,208 control chromosomes in the GnomAD database, including 5,657 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 0.19 (5657 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 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: 0.193 AC: 29350 AN: 152090 Hom.: 5620 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.193 AC: 29446 AN: 152208 Hom.: 5657 Cov.: 33 AF XY: 0.192 AC XY: 14299 AN XY: 74442

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0713

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.175

Alfa AF: 0.143 Hom.: 912

Bravo AF: 0.207

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.7
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6509541; hg19: chr19-51951303;