rs6510489

Positions:

• chr19-35482387-T-C

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 0.245 in 152,064 control chromosomes in the GnomAD database, including 5,101 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 0.25 (5101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.245 AC: 37209 AN: 151946 Hom.: 5092 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.245 AC: 37256 AN: 152064 Hom.: 5101 Cov.: 31 AF XY: 0.241 AC XY: 17929 AN XY: 74334

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0641

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.204

Alfa AF: 0.239 Hom.: 777

Bravo AF: 0.242

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6510489; hg19: chr19-35973289;