rs9729550

Variant names:

• chr1-1199862-A-C
• rs9729550

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 0.391 in 151,986 control chromosomes in the GnomAD database, including 13,702 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 0.39 (13702 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.390 AC: 59248 AN: 151868 Hom.: 13658 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.391 AC: 59351 AN: 151986 Hom.: 13702 Cov.: 33 AF XY: 0.395 AC XY: 29383 AN XY: 74298

African (AFR) AF: 0.563 AC: 23340 AN: 41430

American (AMR) AF: 0.458 AC: 7006 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4404 AN: 5158

South Asian (SAS) AF: 0.447 AC: 2154 AN: 4816

European-Finnish (FIN) AF: 0.254 AC: 2682 AN: 10576

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17795 AN: 67938

Other (OTH) AF: 0.371 AC: 783 AN: 2108

Alfa AF: 0.291 Hom.: 4932

Bravo AF: 0.412

Asia WGS AF: 0.656 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9729550; hg19: chr1-1135242;