rs1751513

Variant names:

• chr1-78727192-A-G
• rs1751513

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 0.877 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.916 AC: 38056 AN: 41536

American (AMR) AF: 0.881 AC: 13467 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3130 AN: 3470

East Asian (EAS) AF: 0.984 AC: 5097 AN: 5178

South Asian (SAS) AF: 0.909 AC: 4387 AN: 4826

European-Finnish (FIN) AF: 0.867 AC: 9174 AN: 10586

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57385 AN: 68010

Other (OTH) AF: 0.895 AC: 1893 AN: 2114

Alfa AF: 0.866 Hom.: 7372

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1751513; hg19: chr1-79192877;