rs2691269

Variant names:

• chr19-51091925-G-A
• rs2691269

Your query was ambiguous. Multiple possible variants found:

• chr19-51091925-G-A
• chr19-51091925-G-C

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 0.158 in 151,860 control chromosomes in the GnomAD database, including 2,063 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 0.16 (2063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 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: 0.158 AC: 23969 AN: 151742 Hom.: 2058 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.158 AC: 23990 AN: 151860 Hom.: 2063 Cov.: 32 AF XY: 0.159 AC XY: 11810 AN XY: 74190

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.137

Alfa AF: 0.135 Hom.: 1778

Bravo AF: 0.146

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2691269; hg19: chr19-51595182;