1-241385280-C-A

Variant names:

• chr1-241385280-C-A
• rs78220092

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.137 AC: 5667 AN: 41430

American (AMR) AF: 0.0173 AC: 264 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5166

South Asian (SAS) AF: 0.0111 AC: 53 AN: 4796

European-Finnish (FIN) AF: 0.00312 AC: 33 AN: 10566

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00682 AC: 464 AN: 68000

Other (OTH) AF: 0.0365 AC: 77 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.39
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs78220092; hg19: chr1-241548580;