1-73588377-C-T

Position:

• chr1-73588377-C-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 0.862 in 151,930 control chromosomes in the GnomAD database, including 56,699 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 0.86 (56699 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.881 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: 0.863 AC: 130948 AN: 151812 Hom.: 56672 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.862 AC: 131032 AN: 151930 Hom.: 56699 Cov.: 30 AF XY: 0.867 AC XY: 64348 AN XY: 74262

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.836

Alfa AF: 0.873 Hom.: 7189

Bravo AF: 0.846

Asia WGS AF: 0.880 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2341260; hg19: chr1-74054060;