rs2414520

Variant names:

• chr15-57784837-G-A
• rs2414520

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.192 in 152,166 control chromosomes in the GnomAD database, including 3,590 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 (3590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29173 AN: 152050 Hom.: 3592 Cov.: 32

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.192 AC: 29166 AN: 152166 Hom.: 3590 Cov.: 32 AF XY: 0.190 AC XY: 14145 AN XY: 74374

African (AFR) AF: 0.0490 AC: 2035 AN: 41530

American (AMR) AF: 0.203 AC: 3111 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3468

East Asian (EAS) AF: 0.0535 AC: 277 AN: 5182

South Asian (SAS) AF: 0.173 AC: 833 AN: 4810

European-Finnish (FIN) AF: 0.234 AC: 2479 AN: 10584

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18916 AN: 67982

Other (OTH) AF: 0.196 AC: 415 AN: 2112

Alfa AF: 0.259 Hom.: 9077

Bravo AF: 0.183

Asia WGS AF: 0.0960 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.74
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2414520; hg19: chr15-58077035;