rs3786776

Variant names:

• chr19-48047590-C-T
• rs3786776

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 0.533 in 152,060 control chromosomes in the GnomAD database, including 23,175 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 0.53 (23175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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: 0.533 AC: 81014 AN: 151942 Hom.: 23165 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.533 AC: 81037 AN: 152060 Hom.: 23175 Cov.: 32 AF XY: 0.537 AC XY: 39932 AN XY: 74346

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.557

Alfa AF: 0.585 Hom.: 53999

Bravo AF: 0.525

Asia WGS AF: 0.722 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3786776; hg19: chr19-48550847;