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
• Publications: 4 publications found

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

African (AFR) AF: 0.0269 AC: 1118 AN: 41550

American (AMR) AF: 0.160 AC: 2442 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3472

East Asian (EAS) AF: 0.0730 AC: 378 AN: 5176

South Asian (SAS) AF: 0.147 AC: 709 AN: 4822

European-Finnish (FIN) AF: 0.176 AC: 1866 AN: 10584

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9884 AN: 68008

Other (OTH) AF: 0.119 AC: 252 AN: 2112

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs3760678; hg19: chr19-7733120;