1-24192153-A-G

Position:

• chr1-24192153-A-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 0.867 in 152,248 control chromosomes in the GnomAD database, including 57,281 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 0.87 (57281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.894 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: 0.867 AC: 131851 AN: 152130 Hom.: 57229 Cov.: 33

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.867 AC: 131957 AN: 152248 Hom.: 57281 Cov.: 33 AF XY: 0.866 AC XY: 64497 AN XY: 74434

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.845

Alfa AF: 0.863 Hom.: 117696

Bravo AF: 0.873

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
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: rs7552167; hg19: chr1-24518643; COSMIC: COSV59525825;