rs1751513

chr1-78727192-A-G

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 0.877 in 152,214 control chromosomes in the GnomAD database, including 58,590 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 0.88 (58590 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133359 AN: 152096 Hom.: 58540 Cov.: 33

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.877 AC: 133466 AN: 152214 Hom.: 58590 Cov.: 33 AF XY: 0.878 AC XY: 65338 AN XY: 74410

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.895

Alfa AF: 0.863 Hom.: 7035

Bravo AF: 0.882

Asia WGS AF: 0.941 AC: 3261 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.54
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1751513; hg19: chr1-79192877;