rs2414391

Variant names:

• chr15-55056093-A-G
• rs2414391

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 68 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0252 AC: 1048 AN: 41578

American (AMR) AF: 0.0224 AC: 342 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3470

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5184

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4824

European-Finnish (FIN) AF: 0.0346 AC: 368 AN: 10622

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0220 AC: 1499 AN: 67990

Other (OTH) AF: 0.0256 AC: 54 AN: 2112

Alfa AF: 0.0214 Hom.: 9

Bravo AF: 0.0238

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.65
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs2414391; hg19: chr15-55348291;