rs3760678

chr19-7668234-A-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 0.114 in 152,204 control chromosomes in the GnomAD database, including 1,226 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 0.11 (1226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 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: 0.114 AC: 17322 AN: 152086 Hom.: 1223 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.114 AC: 17328 AN: 152204 Hom.: 1226 Cov.: 32 AF XY: 0.116 AC XY: 8616 AN XY: 74398

Gnomad4 AFR AF: 0.0269

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0730

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.119

Alfa AF: 0.132 Hom.: 180

Bravo AF: 0.111

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760678; hg19: chr19-7733120;