1-184680369-C-A

Position:

• chr1-184680369-C-A

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 0.0917 in 152,198 control chromosomes in the GnomAD database, including 852 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 0.092 (852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.0916 AC: 13928 AN: 152080 Hom.: 851 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0917 AC: 13954 AN: 152198 Hom.: 852 Cov.: 32 AF XY: 0.0880 AC XY: 6548 AN XY: 74402

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.0482

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0630

Gnomad4 OTH AF: 0.0965

Alfa AF: 0.0689 Hom.: 369

Bravo AF: 0.101

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911628; hg19: chr1-184649503;