1-91572668-C-T

Variant names:

• chr1-91572668-C-T
• rs925192

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 0.801 in 152,022 control chromosomes in the GnomAD database, including 49,089 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 0.80 (49089 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.801 AC: 121711 AN: 151904 Hom.: 49053 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.801 AC: 121799 AN: 152022 Hom.: 49089 Cov.: 31 AF XY: 0.803 AC XY: 59627 AN XY: 74296

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.946

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.806

Alfa AF: 0.818 Hom.: 69349

Bravo AF: 0.807

Asia WGS AF: 0.956 AC: 3323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925192; hg19: chr1-92038225;