rs884409

Positions:

• chr2-171522147-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 0.167 in 1,384,136 control chromosomes in the GnomAD database, including 21,364 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 0.22 (4284 hom., cov: 32)
  • Exomes 𝑓: 0.16 (17080 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.219 AC: 33356 AN: 151988 Hom.: 4272 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.161 AC: 198219 AN: 1232030 Hom.: 17080 AF XY: 0.160 AC XY: 97119 AN XY: 606360

Gnomad4 AFR exome AF: 0.359

Gnomad4 AMR exome AF: 0.0933

Gnomad4 ASJ exome AF: 0.120

Gnomad4 EAS exome AF: 0.123

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.169

GnomAD4 genome AF: 0.220 AC: 33398 AN: 152106 Hom.: 4284 Cov.: 32 AF XY: 0.221 AC XY: 16410 AN XY: 74352

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.188

Alfa AF: 0.206 Hom.: 718

Bravo AF: 0.218

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884409; hg19: chr2-172378657;