rs1578790

Positions:

• chr1-111033299-T-G

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 0.546 in 151,914 control chromosomes in the GnomAD database, including 22,931 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 0.55 (22931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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: 0.546 AC: 82833 AN: 151796 Hom.: 22920 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.546 AC: 82874 AN: 151914 Hom.: 22931 Cov.: 31 AF XY: 0.537 AC XY: 39849 AN XY: 74264

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.536

Alfa AF: 0.555 Hom.: 47710

Bravo AF: 0.553

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1578790; hg19: chr1-111575921;