rs2215383

Variant names:

• chr7-15023358-T-C
• rs2215383

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 0.543 in 152,010 control chromosomes in the GnomAD database, including 22,697 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 0.54 (22697 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.543 AC: 82470 AN: 151890 Hom.: 22687 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.543 AC: 82522 AN: 152010 Hom.: 22697 Cov.: 33 AF XY: 0.539 AC XY: 40057 AN XY: 74300

African (AFR) AF: 0.567 AC: 23537 AN: 41480

American (AMR) AF: 0.481 AC: 7331 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3468

East Asian (EAS) AF: 0.681 AC: 3504 AN: 5148

South Asian (SAS) AF: 0.624 AC: 3012 AN: 4826

European-Finnish (FIN) AF: 0.439 AC: 4636 AN: 10556

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36880 AN: 67966

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.550 Hom.: 29897

Bravo AF: 0.544

Asia WGS AF: 0.636 AC: 2205 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.60
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2215383; hg19: chr7-15062983;