rs61779296

chr1-58577785-G-Achr1-58577785-G-T

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 0.284 in 164,270 control chromosomes in the GnomAD database, including 7,283 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 0.29 (7095 hom., cov: 33)
  • Exomes 𝑓: 0.17 (188 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 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: 0.293 AC: 44427 AN: 151884 Hom.: 7071 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.171 AC: 2098 AN: 12266 Hom.: 188 Cov.: 0 AF XY: 0.173 AC XY: 1023 AN XY: 5904

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.170

Gnomad4 NFE exome AF: 0.191

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.293 AC: 44487 AN: 152004 Hom.: 7095 Cov.: 33 AF XY: 0.282 AC XY: 20975 AN XY: 74340

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.0552

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.294

Alfa AF: 0.277 Hom.: 1218

Bravo AF: 0.302

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.87
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61779296; hg19: chr1-59043457; COSMIC: COSV64666973;