rs7519783

Variant names:

• chr1-200715929-G-A
• rs7519783

Your query was ambiguous. Multiple possible variants found:

• chr1-200715929-G-A
• chr1-200715929-G-C
• chr1-200715929-G-T

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 0.695 in 152,048 control chromosomes in the GnomAD database, including 36,988 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 0.69 (36988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.728 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: 0.695 AC: 105616 AN: 151930 Hom.: 36980 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.695 AC: 105664 AN: 152048 Hom.: 36988 Cov.: 32 AF XY: 0.696 AC XY: 51714 AN XY: 74304

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.718

Alfa AF: 0.713 Hom.: 20728

Bravo AF: 0.695

Asia WGS AF: 0.714 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7519783; hg19: chr1-200685057;