rs3760678

Variant names:

• chr19-7668234-A-G
• rs3760678

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 0.114 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

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 0.0269073 AN: 0.0269073

Gnomad4 AMR AF: 0.160 AC: 0.15988 AN: 0.15988

Gnomad4 ASJ AF: 0.168 AC: 0.168203 AN: 0.168203

Gnomad4 EAS AF: 0.0730 AC: 0.0730294 AN: 0.0730294

Gnomad4 SAS AF: 0.147 AC: 0.147034 AN: 0.147034

Gnomad4 FIN AF: 0.176 AC: 0.176304 AN: 0.176304

Gnomad4 NFE AF: 0.145 AC: 0.145336 AN: 0.145336

Gnomad4 OTH AF: 0.119 AC: 0.119318 AN: 0.119318

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;