rs1999713

Positions:

• chr1-109907555-T-C

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 0.377 in 151,962 control chromosomes in the GnomAD database, including 11,497 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 0.38 (11497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57156 AN: 151844 Hom.: 11476 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.377 AC: 57220 AN: 151962 Hom.: 11497 Cov.: 32 AF XY: 0.383 AC XY: 28452 AN XY: 74264

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.418

Alfa AF: 0.366 Hom.: 1003

Bravo AF: 0.386

Asia WGS AF: 0.579 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999713; hg19: chr1-110450177;