chr1-78789077-C-G

Variant names:

• chr1-78789077-C-G
• rs12730292

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 0.281 in 151,860 control chromosomes in the GnomAD database, including 6,787 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 0.28 (6787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42640 AN: 151740 Hom.: 6784 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.281 AC: 42657 AN: 151860 Hom.: 6787 Cov.: 32 AF XY: 0.281 AC XY: 20878 AN XY: 74208

African (AFR) AF: 0.162 AC: 6733 AN: 41438

American (AMR) AF: 0.322 AC: 4914 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3466

East Asian (EAS) AF: 0.0577 AC: 299 AN: 5178

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4828

European-Finnish (FIN) AF: 0.363 AC: 3816 AN: 10516

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23870 AN: 67874

Other (OTH) AF: 0.262 AC: 551 AN: 2104

Alfa AF: 0.325 Hom.: 4660

Bravo AF: 0.272

Asia WGS AF: 0.165 AC: 578 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.54
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs12730292; hg19: chr1-79254762;