1-182620196-C-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 0.306 in 149,684 control chromosomes in the GnomAD database, including 8,629 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 0.31 (8629 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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: 0.306 AC: 45741 AN: 149586 Hom.: 8594 Cov.: 29

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.306 AC: 45830 AN: 149684 Hom.: 8629 Cov.: 29 AF XY: 0.305 AC XY: 22257 AN XY: 72958

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.250

Alfa AF: 0.248 Hom.: 693

Bravo AF: 0.318

Asia WGS AF: 0.264 AC: 921 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	1.7
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1287820; hg19: chr1-182589331; COSMIC: COSV73690677;