1-194561784-A-G

Position:

• chr1-194561784-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 0.266 in 151,978 control chromosomes in the GnomAD database, including 8,436 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 0.27 (8436 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

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 (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.266 AC: 40353 AN: 151860 Hom.: 8399 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.266 AC: 40437 AN: 151978 Hom.: 8436 Cov.: 31 AF XY: 0.270 AC XY: 20035 AN XY: 74286

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.232

Alfa AF: 0.132 Hom.: 3878

Bravo AF: 0.286

Asia WGS AF: 0.310 AC: 1079 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3001167; hg19: chr1-194530914;