rs1709084

Variant names:

• chr19-41096565-A-G
• rs1709084

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 0.123 in 152,216 control chromosomes in the GnomAD database, including 1,505 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 0.12 (1505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.122 AC: 18604 AN: 152098 Hom.: 1492 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.123 AC: 18661 AN: 152216 Hom.: 1505 Cov.: 32 AF XY: 0.123 AC XY: 9150 AN XY: 74430

African (AFR) AF: 0.207 AC: 8598 AN: 41506

American (AMR) AF: 0.164 AC: 2502 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.0268 AC: 139 AN: 5184

South Asian (SAS) AF: 0.119 AC: 575 AN: 4822

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5488 AN: 68028

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0942 Hom.: 3256

Bravo AF: 0.130

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.26
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1709084; hg19: chr19-41602470;