rs6509541

Variant names:

• chr19-51448049-T-G
• rs6509541

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;