rs1192415

chr1-91611540-G-Achr1-91611540-G-Cchr1-91611540-G-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 0.807 in 151,948 control chromosomes in the GnomAD database, including 49,616 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 0.81 (49616 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.807 AC: 122501 AN: 151830 Hom.: 49580 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.807 AC: 122590 AN: 151948 Hom.: 49616 Cov.: 30 AF XY: 0.807 AC XY: 59928 AN XY: 74254

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.804

Alfa AF: 0.813 Hom.: 72466

Bravo AF: 0.803

Asia WGS AF: 0.786 AC: 2732 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	10
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1192415; hg19: chr1-92077097;