rs78220092

Positions:

• chr1-241385280-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 0.0434 in 152,028 control chromosomes in the GnomAD database, including 388 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 0.043 (388 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

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 = 0.134 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: 0.0433 AC: 6571 AN: 151912 Hom.: 385 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.00312

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00682

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0434 AC: 6600 AN: 152028 Hom.: 388 Cov.: 31 AF XY: 0.0417 AC XY: 3096 AN XY: 74292

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00445

Gnomad4 SAS AF: 0.0111

Gnomad4 FIN AF: 0.00312

Gnomad4 NFE AF: 0.00682

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0204 Hom.: 37

Bravo AF: 0.0491

Asia WGS AF: 0.0230 AC: 80 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	0.62
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78220092; hg19: chr1-241548580;