rs499689

chr1-229429985-A-Gchr1-229429985-A-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 0.368 in 152,106 control chromosomes in the GnomAD database, including 10,537 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 0.37 (10537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 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: 0.368 AC: 55988 AN: 151988 Hom.: 10536 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.368 AC: 56000 AN: 152106 Hom.: 10537 Cov.: 32 AF XY: 0.365 AC XY: 27166 AN XY: 74334

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.384

Alfa AF: 0.404 Hom.: 21700

Bravo AF: 0.366

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.014
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs499689; hg19: chr1-229565732;