rs6510489

Variant names:

• chr19-35482387-T-C
• rs6510489

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 0.245 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.353 AC: 14621 AN: 41450

American (AMR) AF: 0.164 AC: 2509 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0641 AC: 222 AN: 3466

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5180

South Asian (SAS) AF: 0.163 AC: 785 AN: 4824

European-Finnish (FIN) AF: 0.239 AC: 2518 AN: 10556

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15753 AN: 67998

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.238 Hom.: 6421

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6510489; hg19: chr19-35973289;