rs1863080

chr2-36299293-T-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 0.18 in 182,672 control chromosomes in the GnomAD database, including 4,179 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 0.19 (3695 hom., cov: 32)
  • Exomes 𝑓: 0.13 (484 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 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: 0.189 AC: 28750 AN: 151804 Hom.: 3686 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0941

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.0967

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.132 AC: 4059 AN: 30750 Hom.: 484 AF XY: 0.144 AC XY: 2479 AN XY: 17210

Gnomad4 AFR exome AF: 0.301

Gnomad4 AMR exome AF: 0.274

Gnomad4 ASJ exome AF: 0.0760

Gnomad4 EAS exome AF: 0.313

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.0815

Gnomad4 NFE exome AF: 0.0789

Gnomad4 OTH exome AF: 0.122

GnomAD4 genome AF: 0.190 AC: 28799 AN: 151922 Hom.: 3695 Cov.: 32 AF XY: 0.195 AC XY: 14455 AN XY: 74266

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.0941

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.0967

Gnomad4 NFE AF: 0.0928

Gnomad4 OTH AF: 0.170

Alfa AF: 0.142 Hom.: 1226

Bravo AF: 0.204

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.0
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863080; hg19: chr2-36526436;