rs2414391

chr15-55056093-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0243 in 152,270 control chromosomes in the GnomAD database, including 68 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 0.024 (68 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0243 (3696/152270) while in subpopulation AFR AF= 0.0252 (1048/41578). AF 95% confidence interval is 0.0239. There are 68 homozygotes in gnomad4. There are 1856 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 68 gene

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: 0.0242 AC: 3688 AN: 152152 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0243 AC: 3696 AN: 152270 Hom.: 68 Cov.: 32 AF XY: 0.0249 AC XY: 1856 AN XY: 74466

Gnomad4 AFR AF: 0.0252

Gnomad4 AMR AF: 0.0224

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0346

Gnomad4 NFE AF: 0.0220

Gnomad4 OTH AF: 0.0256

Alfa AF: 0.0217 Hom.: 9

Bravo AF: 0.0238

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2414391; hg19: chr15-55348291;