1-13864174-A-G

Position:

• chr1-13864174-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 0.62 in 150,982 control chromosomes in the GnomAD database, including 29,733 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 0.62 (29733 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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: 0.620 AC: 93520 AN: 150864 Hom.: 29700 Cov.: 28

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.620 AC: 93608 AN: 150982 Hom.: 29733 Cov.: 28 AF XY: 0.621 AC XY: 45776 AN XY: 73656

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.633

Alfa AF: 0.672 Hom.: 69705

Bravo AF: 0.613

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720035; hg19: chr1-14190669;