rs990707

Variant names:

• chr1-175809837-G-C
• rs990707

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 0.857 in 152,180 control chromosomes in the GnomAD database, including 56,019 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 0.86 (56019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.857 AC: 130347 AN: 152062 Hom.: 55992 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.857 AC: 130423 AN: 152180 Hom.: 56019 Cov.: 32 AF XY: 0.856 AC XY: 63677 AN XY: 74382

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.872

Alfa AF: 0.849 Hom.: 6816

Bravo AF: 0.856

Asia WGS AF: 0.869 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs990707; hg19: chr1-175778973;